diff --git a/blogdown/en/sp/spr/SPRinstall_cache/html/__packages b/blogdown/en/sp/spr/SPRinstall_cache/html/__packages new file mode 100644 index 000000000..560927c56 --- /dev/null +++ b/blogdown/en/sp/spr/SPRinstall_cache/html/__packages @@ -0,0 +1,3 @@ +base +BiocStyle +magrittr diff --git a/blogdown/en/sp/spr/SPRinstall_cache/html/setup_8554bf6df8df60863ac5aab935273910.RData b/blogdown/en/sp/spr/SPRinstall_cache/html/setup_8554bf6df8df60863ac5aab935273910.RData new file mode 100644 index 000000000..957eacfee Binary files /dev/null and b/blogdown/en/sp/spr/SPRinstall_cache/html/setup_8554bf6df8df60863ac5aab935273910.RData differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/cleaning_099c5009c8c8298a23befa3ba15f24d7.rdb b/blogdown/en/sp/spr/SPRinstall_cache/html/setup_8554bf6df8df60863ac5aab935273910.rdb similarity index 100% rename from blogdown/en/sp/spr/gettingstarted_cache/html/cleaning_099c5009c8c8298a23befa3ba15f24d7.rdb rename to blogdown/en/sp/spr/SPRinstall_cache/html/setup_8554bf6df8df60863ac5aab935273910.rdb diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/cleaning_099c5009c8c8298a23befa3ba15f24d7.rdx b/blogdown/en/sp/spr/SPRinstall_cache/html/setup_8554bf6df8df60863ac5aab935273910.rdx similarity index 100% rename from blogdown/en/sp/spr/gettingstarted_cache/html/cleaning_099c5009c8c8298a23befa3ba15f24d7.rdx rename to blogdown/en/sp/spr/SPRinstall_cache/html/setup_8554bf6df8df60863ac5aab935273910.rdx diff --git a/blogdown/en/sp/spr/SPRinstall_cache/html/spr_install_ed0b32c45b1ec6c9ba18b7f1fc35abd5.RData b/blogdown/en/sp/spr/SPRinstall_cache/html/spr_install_ed0b32c45b1ec6c9ba18b7f1fc35abd5.RData new file mode 100644 index 000000000..f233c13e1 Binary files /dev/null and b/blogdown/en/sp/spr/SPRinstall_cache/html/spr_install_ed0b32c45b1ec6c9ba18b7f1fc35abd5.RData differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/dir_3f0833b061790677c6646f0fcb766916.rdb b/blogdown/en/sp/spr/SPRinstall_cache/html/spr_install_ed0b32c45b1ec6c9ba18b7f1fc35abd5.rdb similarity index 100% rename from blogdown/en/sp/spr/gettingstarted_cache/html/dir_3f0833b061790677c6646f0fcb766916.rdb rename to blogdown/en/sp/spr/SPRinstall_cache/html/spr_install_ed0b32c45b1ec6c9ba18b7f1fc35abd5.rdb diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/dir_3f0833b061790677c6646f0fcb766916.rdx b/blogdown/en/sp/spr/SPRinstall_cache/html/spr_install_ed0b32c45b1ec6c9ba18b7f1fc35abd5.rdx similarity index 100% rename from blogdown/en/sp/spr/gettingstarted_cache/html/dir_3f0833b061790677c6646f0fcb766916.rdx rename to blogdown/en/sp/spr/SPRinstall_cache/html/spr_install_ed0b32c45b1ec6c9ba18b7f1fc35abd5.rdx diff --git a/blogdown/en/sp/spr/SPRinstall_cache/html/spr_install_gh_2b6d5e464b583c5c810abaf808720c6b.RData b/blogdown/en/sp/spr/SPRinstall_cache/html/spr_install_gh_2b6d5e464b583c5c810abaf808720c6b.RData new file mode 100644 index 000000000..690cd8234 Binary files /dev/null and b/blogdown/en/sp/spr/SPRinstall_cache/html/spr_install_gh_2b6d5e464b583c5c810abaf808720c6b.RData differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/documentation_3369537b5da7730cafdc54b7e06bce1a.rdb b/blogdown/en/sp/spr/SPRinstall_cache/html/spr_install_gh_2b6d5e464b583c5c810abaf808720c6b.rdb similarity index 100% rename from blogdown/en/sp/spr/gettingstarted_cache/html/documentation_3369537b5da7730cafdc54b7e06bce1a.rdb rename to blogdown/en/sp/spr/SPRinstall_cache/html/spr_install_gh_2b6d5e464b583c5c810abaf808720c6b.rdb diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/documentation_3369537b5da7730cafdc54b7e06bce1a.rdx b/blogdown/en/sp/spr/SPRinstall_cache/html/spr_install_gh_2b6d5e464b583c5c810abaf808720c6b.rdx similarity index 100% rename from blogdown/en/sp/spr/gettingstarted_cache/html/documentation_3369537b5da7730cafdc54b7e06bce1a.rdx rename to blogdown/en/sp/spr/SPRinstall_cache/html/spr_install_gh_2b6d5e464b583c5c810abaf808720c6b.rdx diff --git a/blogdown/en/sp/spr/SPRinstall_cache/html/table_tools_9e871a9d4d440e5569f5a8245d835a28.RData b/blogdown/en/sp/spr/SPRinstall_cache/html/table_tools_9e871a9d4d440e5569f5a8245d835a28.RData new file mode 100644 index 000000000..e362a944f Binary files /dev/null and b/blogdown/en/sp/spr/SPRinstall_cache/html/table_tools_9e871a9d4d440e5569f5a8245d835a28.RData differ diff --git a/blogdown/en/sp/spr/SPRinstall_cache/html/table_tools_9e871a9d4d440e5569f5a8245d835a28.rdb b/blogdown/en/sp/spr/SPRinstall_cache/html/table_tools_9e871a9d4d440e5569f5a8245d835a28.rdb new file mode 100644 index 000000000..802fe729c Binary files /dev/null and b/blogdown/en/sp/spr/SPRinstall_cache/html/table_tools_9e871a9d4d440e5569f5a8245d835a28.rdb differ diff --git a/blogdown/en/sp/spr/SPRinstall_cache/html/table_tools_9e871a9d4d440e5569f5a8245d835a28.rdx b/blogdown/en/sp/spr/SPRinstall_cache/html/table_tools_9e871a9d4d440e5569f5a8245d835a28.rdx new file mode 100644 index 000000000..1e93f4a4d Binary files /dev/null and b/blogdown/en/sp/spr/SPRinstall_cache/html/table_tools_9e871a9d4d440e5569f5a8245d835a28.rdx differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/__packages b/blogdown/en/sp/spr/cwl_and_spr_cache/html/__packages new file mode 100644 index 000000000..fe74ef528 --- /dev/null +++ b/blogdown/en/sp/spr/cwl_and_spr_cache/html/__packages @@ -0,0 +1,18 @@ +base +BiocStyle +BiocGenerics +S4Vectors +IRanges +GenomeInfoDb +GenomicRanges +XVector +Biostrings +Rsamtools +BiocParallel +matrixStats +MatrixGenerics +Biobase +SummarizedExperiment +GenomicAlignments +ShortRead +systemPipeR diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/cmd_8647f3c24634f286f339e97b5b1d1825.RData b/blogdown/en/sp/spr/cwl_and_spr_cache/html/cmd_8647f3c24634f286f339e97b5b1d1825.RData new file mode 100644 index 000000000..ec17a6eab Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/cmd_8647f3c24634f286f339e97b5b1d1825.RData differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/cmd_8647f3c24634f286f339e97b5b1d1825.rdb b/blogdown/en/sp/spr/cwl_and_spr_cache/html/cmd_8647f3c24634f286f339e97b5b1d1825.rdb new file mode 100644 index 000000000..e1ab54f7c Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/cmd_8647f3c24634f286f339e97b5b1d1825.rdb differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/cmd_8647f3c24634f286f339e97b5b1d1825.rdx b/blogdown/en/sp/spr/cwl_and_spr_cache/html/cmd_8647f3c24634f286f339e97b5b1d1825.rdx new file mode 100644 index 000000000..f0b001f72 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/cmd_8647f3c24634f286f339e97b5b1d1825.rdx differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/fromFile_7a988beda51686a1c5ac71abbff946a0.RData b/blogdown/en/sp/spr/cwl_and_spr_cache/html/fromFile_7a988beda51686a1c5ac71abbff946a0.RData new file mode 100644 index 000000000..6c3bb83c7 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/fromFile_7a988beda51686a1c5ac71abbff946a0.RData differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/fromFile_7a988beda51686a1c5ac71abbff946a0.rdb b/blogdown/en/sp/spr/cwl_and_spr_cache/html/fromFile_7a988beda51686a1c5ac71abbff946a0.rdb new file mode 100644 index 000000000..e4cbc31a1 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/fromFile_7a988beda51686a1c5ac71abbff946a0.rdb differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/fromFile_7a988beda51686a1c5ac71abbff946a0.rdx b/blogdown/en/sp/spr/cwl_and_spr_cache/html/fromFile_7a988beda51686a1c5ac71abbff946a0.rdx new file mode 100644 index 000000000..e3e31ba81 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/fromFile_7a988beda51686a1c5ac71abbff946a0.rdx differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/fromFile_example_1b555c44be60a54b3033b2114ccf1fa2.RData b/blogdown/en/sp/spr/cwl_and_spr_cache/html/fromFile_example_1b555c44be60a54b3033b2114ccf1fa2.RData new file mode 100644 index 000000000..ecfcb174a Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/fromFile_example_1b555c44be60a54b3033b2114ccf1fa2.RData differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/fromFile_example_1b555c44be60a54b3033b2114ccf1fa2.rdb b/blogdown/en/sp/spr/cwl_and_spr_cache/html/fromFile_example_1b555c44be60a54b3033b2114ccf1fa2.rdb new file mode 100644 index 000000000..82e52028e Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/fromFile_example_1b555c44be60a54b3033b2114ccf1fa2.rdb differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/fromFile_example_1b555c44be60a54b3033b2114ccf1fa2.rdx b/blogdown/en/sp/spr/cwl_and_spr_cache/html/fromFile_example_1b555c44be60a54b3033b2114ccf1fa2.rdx new file mode 100644 index 000000000..d70775416 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/fromFile_example_1b555c44be60a54b3033b2114ccf1fa2.rdx differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/saving_2d299f30249cc0d5e41333077c76e8e3.RData b/blogdown/en/sp/spr/cwl_and_spr_cache/html/saving_2d299f30249cc0d5e41333077c76e8e3.RData new file mode 100644 index 000000000..ae5573815 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/saving_2d299f30249cc0d5e41333077c76e8e3.RData differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/documentation_cf1d4843db726ce663b2bf916e2f450b.rdb b/blogdown/en/sp/spr/cwl_and_spr_cache/html/saving_2d299f30249cc0d5e41333077c76e8e3.rdb similarity index 100% rename from blogdown/en/sp/spr/gettingstarted_cache/html/documentation_cf1d4843db726ce663b2bf916e2f450b.rdb rename to blogdown/en/sp/spr/cwl_and_spr_cache/html/saving_2d299f30249cc0d5e41333077c76e8e3.rdb diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/documentation_cf1d4843db726ce663b2bf916e2f450b.rdx b/blogdown/en/sp/spr/cwl_and_spr_cache/html/saving_2d299f30249cc0d5e41333077c76e8e3.rdx similarity index 100% rename from blogdown/en/sp/spr/gettingstarted_cache/html/documentation_cf1d4843db726ce663b2bf916e2f450b.rdx rename to blogdown/en/sp/spr/cwl_and_spr_cache/html/saving_2d299f30249cc0d5e41333077c76e8e3.rdx diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/setup_bd6c1bf6973b99e71a771d4e62b92047.RData b/blogdown/en/sp/spr/cwl_and_spr_cache/html/setup_bd6c1bf6973b99e71a771d4e62b92047.RData new file mode 100644 index 000000000..7e27f2bab Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/setup_bd6c1bf6973b99e71a771d4e62b92047.RData differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/install_0ebfe8510aceb616bf6e78aee75d88e2.rdb b/blogdown/en/sp/spr/cwl_and_spr_cache/html/setup_bd6c1bf6973b99e71a771d4e62b92047.rdb similarity index 100% rename from blogdown/en/sp/spr/gettingstarted_cache/html/install_0ebfe8510aceb616bf6e78aee75d88e2.rdb rename to blogdown/en/sp/spr/cwl_and_spr_cache/html/setup_bd6c1bf6973b99e71a771d4e62b92047.rdb diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/install_0ebfe8510aceb616bf6e78aee75d88e2.rdx b/blogdown/en/sp/spr/cwl_and_spr_cache/html/setup_bd6c1bf6973b99e71a771d4e62b92047.rdx similarity index 100% rename from blogdown/en/sp/spr/gettingstarted_cache/html/install_0ebfe8510aceb616bf6e78aee75d88e2.rdx rename to blogdown/en/sp/spr/cwl_and_spr_cache/html/setup_bd6c1bf6973b99e71a771d4e62b92047.rdx diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/sprCWL_573b4ccede3d1318f305a55df0d7d7b6.RData b/blogdown/en/sp/spr/cwl_and_spr_cache/html/sprCWL_573b4ccede3d1318f305a55df0d7d7b6.RData new file mode 100644 index 000000000..81ed68c3f Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/sprCWL_573b4ccede3d1318f305a55df0d7d7b6.RData differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/install_7b263913cc8ee3c735574321403e08b8.rdb b/blogdown/en/sp/spr/cwl_and_spr_cache/html/sprCWL_573b4ccede3d1318f305a55df0d7d7b6.rdb similarity index 100% rename from blogdown/en/sp/spr/gettingstarted_cache/html/install_7b263913cc8ee3c735574321403e08b8.rdb rename to blogdown/en/sp/spr/cwl_and_spr_cache/html/sprCWL_573b4ccede3d1318f305a55df0d7d7b6.rdb diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/install_7b263913cc8ee3c735574321403e08b8.rdx b/blogdown/en/sp/spr/cwl_and_spr_cache/html/sprCWL_573b4ccede3d1318f305a55df0d7d7b6.rdx similarity index 100% rename from blogdown/en/sp/spr/gettingstarted_cache/html/install_7b263913cc8ee3c735574321403e08b8.rdx rename to blogdown/en/sp/spr/cwl_and_spr_cache/html/sprCWL_573b4ccede3d1318f305a55df0d7d7b6.rdx diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-10_254288b1863220aad693e0a161d4d01a.RData b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-10_254288b1863220aad693e0a161d4d01a.RData new file mode 100644 index 000000000..1eb6664bb Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-10_254288b1863220aad693e0a161d4d01a.RData differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/setup_364d4b0afd20170202ebe6c445f9700f.rdb b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-10_254288b1863220aad693e0a161d4d01a.rdb similarity index 100% rename from blogdown/en/sp/spr/gettingstarted_cache/html/setup_364d4b0afd20170202ebe6c445f9700f.rdb rename to blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-10_254288b1863220aad693e0a161d4d01a.rdb diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/setup_364d4b0afd20170202ebe6c445f9700f.rdx b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-10_254288b1863220aad693e0a161d4d01a.rdx similarity index 100% rename from blogdown/en/sp/spr/gettingstarted_cache/html/setup_364d4b0afd20170202ebe6c445f9700f.rdx rename to blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-10_254288b1863220aad693e0a161d4d01a.rdx diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-11_562d9ac1a4c0149dc624b3d9bdb5b2f7.RData b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-11_562d9ac1a4c0149dc624b3d9bdb5b2f7.RData new file mode 100644 index 000000000..ff70bcfdd Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-11_562d9ac1a4c0149dc624b3d9bdb5b2f7.RData differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/setup_b2105ac0d2ccba413cf8eafdb5073f26.rdb b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-11_562d9ac1a4c0149dc624b3d9bdb5b2f7.rdb similarity index 100% rename from blogdown/en/sp/spr/gettingstarted_cache/html/setup_b2105ac0d2ccba413cf8eafdb5073f26.rdb rename to blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-11_562d9ac1a4c0149dc624b3d9bdb5b2f7.rdb diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/setup_b2105ac0d2ccba413cf8eafdb5073f26.rdx b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-11_562d9ac1a4c0149dc624b3d9bdb5b2f7.rdx similarity index 100% rename from blogdown/en/sp/spr/gettingstarted_cache/html/setup_b2105ac0d2ccba413cf8eafdb5073f26.rdx rename to blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-11_562d9ac1a4c0149dc624b3d9bdb5b2f7.rdx diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-12_6f3df6dfbed410d1649bd70a4cf4f9f2.RData b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-12_6f3df6dfbed410d1649bd70a4cf4f9f2.RData new file mode 100644 index 000000000..c367043d6 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-12_6f3df6dfbed410d1649bd70a4cf4f9f2.RData differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsFig_5c9371815426b7b2e17a029843a1690b.rdb b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-12_6f3df6dfbed410d1649bd70a4cf4f9f2.rdb similarity index 100% rename from blogdown/en/sp/spr/gettingstarted_cache/html/targetsFig_5c9371815426b7b2e17a029843a1690b.rdb rename to blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-12_6f3df6dfbed410d1649bd70a4cf4f9f2.rdb diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsFig_5c9371815426b7b2e17a029843a1690b.rdx b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-12_6f3df6dfbed410d1649bd70a4cf4f9f2.rdx similarity index 100% rename from blogdown/en/sp/spr/gettingstarted_cache/html/targetsFig_5c9371815426b7b2e17a029843a1690b.rdx rename to blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-12_6f3df6dfbed410d1649bd70a4cf4f9f2.rdx diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-1_3637c76f278eea2e30ee682137ae64dd.RData b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-1_3637c76f278eea2e30ee682137ae64dd.RData new file mode 100644 index 000000000..63b6a9aff Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-1_3637c76f278eea2e30ee682137ae64dd.RData differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-1_3637c76f278eea2e30ee682137ae64dd.rdb b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-1_3637c76f278eea2e30ee682137ae64dd.rdb new file mode 100644 index 000000000..0c02e43c8 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-1_3637c76f278eea2e30ee682137ae64dd.rdb differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-1_3637c76f278eea2e30ee682137ae64dd.rdx b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-1_3637c76f278eea2e30ee682137ae64dd.rdx new file mode 100644 index 000000000..73e9013ee Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-1_3637c76f278eea2e30ee682137ae64dd.rdx differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-2_8fbdfb7ab02202bbb3a4669b224e64ad.RData b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-2_8fbdfb7ab02202bbb3a4669b224e64ad.RData new file mode 100644 index 000000000..320d97291 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-2_8fbdfb7ab02202bbb3a4669b224e64ad.RData differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-2_8fbdfb7ab02202bbb3a4669b224e64ad.rdb b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-2_8fbdfb7ab02202bbb3a4669b224e64ad.rdb new file mode 100644 index 000000000..ed1c42893 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-2_8fbdfb7ab02202bbb3a4669b224e64ad.rdb differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-2_8fbdfb7ab02202bbb3a4669b224e64ad.rdx b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-2_8fbdfb7ab02202bbb3a4669b224e64ad.rdx new file mode 100644 index 000000000..732712df8 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-2_8fbdfb7ab02202bbb3a4669b224e64ad.rdx differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-3_4669f51f2d06a5ff2424307335b510e7.RData b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-3_4669f51f2d06a5ff2424307335b510e7.RData new file mode 100644 index 000000000..15aedeea5 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-3_4669f51f2d06a5ff2424307335b510e7.RData differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-3_4669f51f2d06a5ff2424307335b510e7.rdb b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-3_4669f51f2d06a5ff2424307335b510e7.rdb new file mode 100644 index 000000000..31024774c Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-3_4669f51f2d06a5ff2424307335b510e7.rdb differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-3_4669f51f2d06a5ff2424307335b510e7.rdx b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-3_4669f51f2d06a5ff2424307335b510e7.rdx new file mode 100644 index 000000000..c1794c4e2 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-3_4669f51f2d06a5ff2424307335b510e7.rdx differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-4_6b121f769a440d9356ebd7e14395c2d7.RData b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-4_6b121f769a440d9356ebd7e14395c2d7.RData new file mode 100644 index 000000000..5b57d14ef Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-4_6b121f769a440d9356ebd7e14395c2d7.RData differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetscomp_a16aec4247ee217dbaf82f15ba34e9d0.rdb b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-4_6b121f769a440d9356ebd7e14395c2d7.rdb similarity index 100% rename from blogdown/en/sp/spr/gettingstarted_cache/html/targetscomp_a16aec4247ee217dbaf82f15ba34e9d0.rdb rename to blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-4_6b121f769a440d9356ebd7e14395c2d7.rdb diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetscomp_a16aec4247ee217dbaf82f15ba34e9d0.rdx b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-4_6b121f769a440d9356ebd7e14395c2d7.rdx similarity index 100% rename from blogdown/en/sp/spr/gettingstarted_cache/html/targetscomp_a16aec4247ee217dbaf82f15ba34e9d0.rdx rename to blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-4_6b121f769a440d9356ebd7e14395c2d7.rdx diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-5_f2003fcccde8bf1b68dad8759d8307a0.RData b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-5_f2003fcccde8bf1b68dad8759d8307a0.RData new file mode 100644 index 000000000..53856b157 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-5_f2003fcccde8bf1b68dad8759d8307a0.RData differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-5_f2003fcccde8bf1b68dad8759d8307a0.rdb b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-5_f2003fcccde8bf1b68dad8759d8307a0.rdb new file mode 100644 index 000000000..65ff4d0f3 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-5_f2003fcccde8bf1b68dad8759d8307a0.rdb differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-5_f2003fcccde8bf1b68dad8759d8307a0.rdx b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-5_f2003fcccde8bf1b68dad8759d8307a0.rdx new file mode 100644 index 000000000..071b9e61f Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-5_f2003fcccde8bf1b68dad8759d8307a0.rdx differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-6_f867ffd750ab31b87b2fc1a705f836cb.RData b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-6_f867ffd750ab31b87b2fc1a705f836cb.RData new file mode 100644 index 000000000..5f8b423cb Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-6_f867ffd750ab31b87b2fc1a705f836cb.RData differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-6_f867ffd750ab31b87b2fc1a705f836cb.rdb b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-6_f867ffd750ab31b87b2fc1a705f836cb.rdb new file mode 100644 index 000000000..6ffa88467 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-6_f867ffd750ab31b87b2fc1a705f836cb.rdb differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-6_f867ffd750ab31b87b2fc1a705f836cb.rdx b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-6_f867ffd750ab31b87b2fc1a705f836cb.rdx new file mode 100644 index 000000000..33d46b383 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-6_f867ffd750ab31b87b2fc1a705f836cb.rdx differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-7_ba0b20103b2b53a332834a503a82d1c6.RData b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-7_ba0b20103b2b53a332834a503a82d1c6.RData new file mode 100644 index 000000000..0881c6a41 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-7_ba0b20103b2b53a332834a503a82d1c6.RData differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-7_ba0b20103b2b53a332834a503a82d1c6.rdb b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-7_ba0b20103b2b53a332834a503a82d1c6.rdb new file mode 100644 index 000000000..3a4e4eb18 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-7_ba0b20103b2b53a332834a503a82d1c6.rdb differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-7_ba0b20103b2b53a332834a503a82d1c6.rdx b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-7_ba0b20103b2b53a332834a503a82d1c6.rdx new file mode 100644 index 000000000..867f168d5 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-7_ba0b20103b2b53a332834a503a82d1c6.rdx differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-8_212fc6a35e2c23a66fbd86b67c37af93.RData b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-8_212fc6a35e2c23a66fbd86b67c37af93.RData new file mode 100644 index 000000000..9b69e5592 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-8_212fc6a35e2c23a66fbd86b67c37af93.RData differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-8_212fc6a35e2c23a66fbd86b67c37af93.rdb b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-8_212fc6a35e2c23a66fbd86b67c37af93.rdb new file mode 100644 index 000000000..1fb2581e4 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-8_212fc6a35e2c23a66fbd86b67c37af93.rdb differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-8_212fc6a35e2c23a66fbd86b67c37af93.rdx b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-8_212fc6a35e2c23a66fbd86b67c37af93.rdx new file mode 100644 index 000000000..adc40c023 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-8_212fc6a35e2c23a66fbd86b67c37af93.rdx differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-9_79cbafb0b324cc2b4cb6f9e4a5758c2d.RData b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-9_79cbafb0b324cc2b4cb6f9e4a5758c2d.RData new file mode 100644 index 000000000..3d85f65f1 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-9_79cbafb0b324cc2b4cb6f9e4a5758c2d.RData differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-9_79cbafb0b324cc2b4cb6f9e4a5758c2d.rdb b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-9_79cbafb0b324cc2b4cb6f9e4a5758c2d.rdb new file mode 100644 index 000000000..06a29fe45 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-9_79cbafb0b324cc2b4cb6f9e4a5758c2d.rdb differ diff --git a/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-9_79cbafb0b324cc2b4cb6f9e4a5758c2d.rdx b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-9_79cbafb0b324cc2b4cb6f9e4a5758c2d.rdx new file mode 100644 index 000000000..4e110022c Binary files /dev/null and b/blogdown/en/sp/spr/cwl_and_spr_cache/html/unnamed-chunk-9_79cbafb0b324cc2b4cb6f9e4a5758c2d.rdx differ diff --git a/blogdown/en/sp/spr/cwl_syntax_cache/html/__packages b/blogdown/en/sp/spr/cwl_syntax_cache/html/__packages new file mode 100644 index 000000000..400c69a17 --- /dev/null +++ b/blogdown/en/sp/spr/cwl_syntax_cache/html/__packages @@ -0,0 +1,22 @@ +base +BiocStyle +BiocGenerics +S4Vectors +IRanges +GenomeInfoDb +GenomicRanges +XVector +Biostrings +Rsamtools +BiocParallel +matrixStats +MatrixGenerics +Biobase +SummarizedExperiment +GenomicAlignments +ShortRead +systemPipeR +ggplot2 +ape +batchtools +magrittr diff --git a/blogdown/en/sp/spr/cwl_syntax_cache/html/setup_f6425e5fdb93d4f1c87289d40be83e93.RData b/blogdown/en/sp/spr/cwl_syntax_cache/html/setup_f6425e5fdb93d4f1c87289d40be83e93.RData new file mode 100644 index 000000000..3b62d489a Binary files /dev/null and b/blogdown/en/sp/spr/cwl_syntax_cache/html/setup_f6425e5fdb93d4f1c87289d40be83e93.RData differ diff --git a/content/en/sp/spr/steps_cache/html/align_stats1_6e425d027079265be0428b9b061929a9.rdb b/blogdown/en/sp/spr/cwl_syntax_cache/html/setup_f6425e5fdb93d4f1c87289d40be83e93.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/align_stats1_6e425d027079265be0428b9b061929a9.rdb rename to blogdown/en/sp/spr/cwl_syntax_cache/html/setup_f6425e5fdb93d4f1c87289d40be83e93.rdb diff --git a/content/en/sp/spr/steps_cache/html/align_stats1_6e425d027079265be0428b9b061929a9.rdx b/blogdown/en/sp/spr/cwl_syntax_cache/html/setup_f6425e5fdb93d4f1c87289d40be83e93.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/align_stats1_6e425d027079265be0428b9b061929a9.rdx rename to blogdown/en/sp/spr/cwl_syntax_cache/html/setup_f6425e5fdb93d4f1c87289d40be83e93.rdx diff --git a/blogdown/en/sp/spr/cwl_syntax_cache/html/sysargslistImage_4a77d472d2b5fd188374b09f78fc622d.RData b/blogdown/en/sp/spr/cwl_syntax_cache/html/sysargslistImage_4a77d472d2b5fd188374b09f78fc622d.RData new file mode 100644 index 000000000..91e558db8 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_syntax_cache/html/sysargslistImage_4a77d472d2b5fd188374b09f78fc622d.RData differ diff --git a/content/en/sp/spr/steps_cache/html/align_stats2_206329667a843ede0f348976a3373d75.rdb b/blogdown/en/sp/spr/cwl_syntax_cache/html/sysargslistImage_4a77d472d2b5fd188374b09f78fc622d.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/align_stats2_206329667a843ede0f348976a3373d75.rdb rename to blogdown/en/sp/spr/cwl_syntax_cache/html/sysargslistImage_4a77d472d2b5fd188374b09f78fc622d.rdb diff --git a/content/en/sp/spr/steps_cache/html/align_stats2_206329667a843ede0f348976a3373d75.rdx b/blogdown/en/sp/spr/cwl_syntax_cache/html/sysargslistImage_4a77d472d2b5fd188374b09f78fc622d.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/align_stats2_206329667a843ede0f348976a3373d75.rdx rename to blogdown/en/sp/spr/cwl_syntax_cache/html/sysargslistImage_4a77d472d2b5fd188374b09f78fc622d.rdx diff --git a/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-10_c0e7f0497cc06fb9c187ccdfdbfa9679.RData b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-10_c0e7f0497cc06fb9c187ccdfdbfa9679.RData new file mode 100644 index 000000000..b396a26ad Binary files /dev/null and b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-10_c0e7f0497cc06fb9c187ccdfdbfa9679.RData differ diff --git a/content/en/sp/spr/steps_cache/html/align_stats_parallel_6ddd1cc8f83287812e4b39a8e7fa882b.rdb b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-10_c0e7f0497cc06fb9c187ccdfdbfa9679.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/align_stats_parallel_6ddd1cc8f83287812e4b39a8e7fa882b.rdb rename to blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-10_c0e7f0497cc06fb9c187ccdfdbfa9679.rdb diff --git a/content/en/sp/spr/steps_cache/html/align_stats_parallel_6ddd1cc8f83287812e4b39a8e7fa882b.rdx b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-10_c0e7f0497cc06fb9c187ccdfdbfa9679.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/align_stats_parallel_6ddd1cc8f83287812e4b39a8e7fa882b.rdx rename to blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-10_c0e7f0497cc06fb9c187ccdfdbfa9679.rdx diff --git a/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-11_d7e9dde92d75d3dc2df0b2cecf51050e.RData b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-11_d7e9dde92d75d3dc2df0b2cecf51050e.RData new file mode 100644 index 000000000..16eb36ab6 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-11_d7e9dde92d75d3dc2df0b2cecf51050e.RData differ diff --git a/content/en/sp/spr/steps_cache/html/align_stats_parallel_cluster_4a193b9254d3c3fe1d20387fdfa0c528.rdb b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-11_d7e9dde92d75d3dc2df0b2cecf51050e.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/align_stats_parallel_cluster_4a193b9254d3c3fe1d20387fdfa0c528.rdb rename to blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-11_d7e9dde92d75d3dc2df0b2cecf51050e.rdb diff --git a/content/en/sp/spr/steps_cache/html/align_stats_parallel_cluster_4a193b9254d3c3fe1d20387fdfa0c528.rdx b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-11_d7e9dde92d75d3dc2df0b2cecf51050e.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/align_stats_parallel_cluster_4a193b9254d3c3fe1d20387fdfa0c528.rdx rename to blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-11_d7e9dde92d75d3dc2df0b2cecf51050e.rdx diff --git a/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-12_4bc9a4053f1a375926d500df16430206.RData b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-12_4bc9a4053f1a375926d500df16430206.RData new file mode 100644 index 000000000..3cd9f802d Binary files /dev/null and b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-12_4bc9a4053f1a375926d500df16430206.RData differ diff --git a/content/en/sp/spr/steps_cache/html/bowtie2_SYSargs2_31f13017dcefa8ecddf8e70e9cd6b8cc.rdb b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-12_4bc9a4053f1a375926d500df16430206.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/bowtie2_SYSargs2_31f13017dcefa8ecddf8e70e9cd6b8cc.rdb rename to blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-12_4bc9a4053f1a375926d500df16430206.rdb diff --git a/content/en/sp/spr/steps_cache/html/bowtie2_SYSargs2_31f13017dcefa8ecddf8e70e9cd6b8cc.rdx b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-12_4bc9a4053f1a375926d500df16430206.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/bowtie2_SYSargs2_31f13017dcefa8ecddf8e70e9cd6b8cc.rdx rename to blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-12_4bc9a4053f1a375926d500df16430206.rdx diff --git a/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-1_e0d2518256449035114ca43fd205bb34.RData b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-1_e0d2518256449035114ca43fd205bb34.RData new file mode 100644 index 000000000..cb0e12236 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-1_e0d2518256449035114ca43fd205bb34.RData differ diff --git a/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-1_e0d2518256449035114ca43fd205bb34.rdb b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-1_e0d2518256449035114ca43fd205bb34.rdb new file mode 100644 index 000000000..7984afd11 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-1_e0d2518256449035114ca43fd205bb34.rdb differ diff --git a/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-1_e0d2518256449035114ca43fd205bb34.rdx b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-1_e0d2518256449035114ca43fd205bb34.rdx new file mode 100644 index 000000000..15680a9f8 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-1_e0d2518256449035114ca43fd205bb34.rdx differ diff --git a/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-2_e1c7d0d19e98268acafa9b08e88f4cc3.RData b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-2_e1c7d0d19e98268acafa9b08e88f4cc3.RData new file mode 100644 index 000000000..cdc198e89 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-2_e1c7d0d19e98268acafa9b08e88f4cc3.RData differ diff --git a/content/en/sp/spr/steps_cache/html/bowtie2_cluster_0e5f9f8827f83e36bdce0e82a5e4b271.rdb b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-2_e1c7d0d19e98268acafa9b08e88f4cc3.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/bowtie2_cluster_0e5f9f8827f83e36bdce0e82a5e4b271.rdb rename to blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-2_e1c7d0d19e98268acafa9b08e88f4cc3.rdb diff --git a/content/en/sp/spr/steps_cache/html/bowtie2_cluster_0e5f9f8827f83e36bdce0e82a5e4b271.rdx b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-2_e1c7d0d19e98268acafa9b08e88f4cc3.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/bowtie2_cluster_0e5f9f8827f83e36bdce0e82a5e4b271.rdx rename to blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-2_e1c7d0d19e98268acafa9b08e88f4cc3.rdx diff --git a/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-3_3f2f1f3390a0c8029d9922f16935668f.RData b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-3_3f2f1f3390a0c8029d9922f16935668f.RData new file mode 100644 index 000000000..4c0e6aca8 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-3_3f2f1f3390a0c8029d9922f16935668f.RData differ diff --git a/content/en/sp/spr/steps_cache/html/bowtie2_index_7f826e8bfa28138ff85f9fb1fba0804d.rdb b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-3_3f2f1f3390a0c8029d9922f16935668f.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/bowtie2_index_7f826e8bfa28138ff85f9fb1fba0804d.rdb rename to blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-3_3f2f1f3390a0c8029d9922f16935668f.rdb diff --git a/content/en/sp/spr/steps_cache/html/bowtie2_index_7f826e8bfa28138ff85f9fb1fba0804d.rdx b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-3_3f2f1f3390a0c8029d9922f16935668f.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/bowtie2_index_7f826e8bfa28138ff85f9fb1fba0804d.rdx rename to blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-3_3f2f1f3390a0c8029d9922f16935668f.rdx diff --git a/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-4_83d550da57123d3e692603835945f79a.RData b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-4_83d550da57123d3e692603835945f79a.RData new file mode 100644 index 000000000..cb4f8a385 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-4_83d550da57123d3e692603835945f79a.RData differ diff --git a/content/en/sp/spr/steps_cache/html/bowtie2_sm_72f3af538b704311ef8c8291da780a81.rdb b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-4_83d550da57123d3e692603835945f79a.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/bowtie2_sm_72f3af538b704311ef8c8291da780a81.rdb rename to blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-4_83d550da57123d3e692603835945f79a.rdb diff --git a/content/en/sp/spr/steps_cache/html/bowtie2_sm_72f3af538b704311ef8c8291da780a81.rdx b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-4_83d550da57123d3e692603835945f79a.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/bowtie2_sm_72f3af538b704311ef8c8291da780a81.rdx rename to blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-4_83d550da57123d3e692603835945f79a.rdx diff --git a/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-5_a9c9d5f66640fd92f7702ad04213d846.RData b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-5_a9c9d5f66640fd92f7702ad04213d846.RData new file mode 100644 index 000000000..a1619cf42 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-5_a9c9d5f66640fd92f7702ad04213d846.RData differ diff --git a/content/en/sp/spr/steps_cache/html/bowtie_index_6e801a7d652bf85f09e7272fe4b5df45.rdb b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-5_a9c9d5f66640fd92f7702ad04213d846.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/bowtie_index_6e801a7d652bf85f09e7272fe4b5df45.rdb rename to blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-5_a9c9d5f66640fd92f7702ad04213d846.rdb diff --git a/content/en/sp/spr/steps_cache/html/bowtie_index_6e801a7d652bf85f09e7272fe4b5df45.rdx b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-5_a9c9d5f66640fd92f7702ad04213d846.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/bowtie_index_6e801a7d652bf85f09e7272fe4b5df45.rdx rename to blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-5_a9c9d5f66640fd92f7702ad04213d846.rdx diff --git a/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-6_691650d13355ffeeddc7c2646fabbe7d.RData b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-6_691650d13355ffeeddc7c2646fabbe7d.RData new file mode 100644 index 000000000..47f5ea2d3 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-6_691650d13355ffeeddc7c2646fabbe7d.RData differ diff --git a/content/en/sp/spr/steps_cache/html/bwa-pe_alignment_0a3503d3dc6a5034457f393fcd91e102.rdb b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-6_691650d13355ffeeddc7c2646fabbe7d.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/bwa-pe_alignment_0a3503d3dc6a5034457f393fcd91e102.rdb rename to blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-6_691650d13355ffeeddc7c2646fabbe7d.rdb diff --git a/content/en/sp/spr/steps_cache/html/bwa-pe_alignment_0a3503d3dc6a5034457f393fcd91e102.rdx b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-6_691650d13355ffeeddc7c2646fabbe7d.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/bwa-pe_alignment_0a3503d3dc6a5034457f393fcd91e102.rdx rename to blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-6_691650d13355ffeeddc7c2646fabbe7d.rdx diff --git a/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-7_7004a3496142fd70c0da8423c979ac50.RData b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-7_7004a3496142fd70c0da8423c979ac50.RData new file mode 100644 index 000000000..a1f65ac7d Binary files /dev/null and b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-7_7004a3496142fd70c0da8423c979ac50.RData differ diff --git a/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-7_7004a3496142fd70c0da8423c979ac50.rdb b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-7_7004a3496142fd70c0da8423c979ac50.rdb new file mode 100644 index 000000000..30d904727 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-7_7004a3496142fd70c0da8423c979ac50.rdb differ diff --git a/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-7_7004a3496142fd70c0da8423c979ac50.rdx b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-7_7004a3496142fd70c0da8423c979ac50.rdx new file mode 100644 index 000000000..41d7bef66 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-7_7004a3496142fd70c0da8423c979ac50.rdx differ diff --git a/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-8_1419ee623e5d95e05d4b9cdeaba06cc9.RData b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-8_1419ee623e5d95e05d4b9cdeaba06cc9.RData new file mode 100644 index 000000000..7e719e2c2 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-8_1419ee623e5d95e05d4b9cdeaba06cc9.RData differ diff --git a/content/en/sp/spr/steps_cache/html/bwa_index_8012e619b7f89c3bcf4e5a1f32d78057.rdb b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-8_1419ee623e5d95e05d4b9cdeaba06cc9.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/bwa_index_8012e619b7f89c3bcf4e5a1f32d78057.rdb rename to blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-8_1419ee623e5d95e05d4b9cdeaba06cc9.rdb diff --git a/content/en/sp/spr/steps_cache/html/bwa_index_8012e619b7f89c3bcf4e5a1f32d78057.rdx b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-8_1419ee623e5d95e05d4b9cdeaba06cc9.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/bwa_index_8012e619b7f89c3bcf4e5a1f32d78057.rdx rename to blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-8_1419ee623e5d95e05d4b9cdeaba06cc9.rdx diff --git a/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-9_d0114035a6e9941e2d51340ed9c5fbfa.RData b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-9_d0114035a6e9941e2d51340ed9c5fbfa.RData new file mode 100644 index 000000000..38177b642 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-9_d0114035a6e9941e2d51340ed9c5fbfa.RData differ diff --git a/content/en/sp/spr/steps_cache/html/clusterRun_args_ad7fc3ced89063c2d9a2708058e9e159.rdb b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-9_d0114035a6e9941e2d51340ed9c5fbfa.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/clusterRun_args_ad7fc3ced89063c2d9a2708058e9e159.rdb rename to blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-9_d0114035a6e9941e2d51340ed9c5fbfa.rdb diff --git a/content/en/sp/spr/steps_cache/html/clusterRun_args_ad7fc3ced89063c2d9a2708058e9e159.rdx b/blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-9_d0114035a6e9941e2d51340ed9c5fbfa.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/clusterRun_args_ad7fc3ced89063c2d9a2708058e9e159.rdx rename to blogdown/en/sp/spr/cwl_syntax_cache/html/unnamed-chunk-9_d0114035a6e9941e2d51340ed9c5fbfa.rdx diff --git a/blogdown/en/sp/spr/cwl_syntax_cache/html/utilities_52eb2521606b0d36c64b2830e8402e7b.RData b/blogdown/en/sp/spr/cwl_syntax_cache/html/utilities_52eb2521606b0d36c64b2830e8402e7b.RData new file mode 100644 index 000000000..2789ad740 Binary files /dev/null and b/blogdown/en/sp/spr/cwl_syntax_cache/html/utilities_52eb2521606b0d36c64b2830e8402e7b.RData differ diff --git a/content/en/sp/spr/steps_cache/html/construct_SYSargs2_trim-pe_947cd154bf9a4f037f5d3369680b2b09.rdb b/blogdown/en/sp/spr/cwl_syntax_cache/html/utilities_52eb2521606b0d36c64b2830e8402e7b.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/construct_SYSargs2_trim-pe_947cd154bf9a4f037f5d3369680b2b09.rdb rename to blogdown/en/sp/spr/cwl_syntax_cache/html/utilities_52eb2521606b0d36c64b2830e8402e7b.rdb diff --git a/content/en/sp/spr/steps_cache/html/construct_SYSargs2_trim-pe_947cd154bf9a4f037f5d3369680b2b09.rdx b/blogdown/en/sp/spr/cwl_syntax_cache/html/utilities_52eb2521606b0d36c64b2830e8402e7b.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/construct_SYSargs2_trim-pe_947cd154bf9a4f037f5d3369680b2b09.rdx rename to blogdown/en/sp/spr/cwl_syntax_cache/html/utilities_52eb2521606b0d36c64b2830e8402e7b.rdx diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/cleaning_099c5009c8c8298a23befa3ba15f24d7.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/cleaning_099c5009c8c8298a23befa3ba15f24d7.RData deleted file mode 100644 index 4a2dca944..000000000 Binary files a/blogdown/en/sp/spr/gettingstarted_cache/html/cleaning_099c5009c8c8298a23befa3ba15f24d7.RData and /dev/null differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/cleaning_af88f1bc1bb0e2057ad9574402ceed22.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/cleaning_af88f1bc1bb0e2057ad9574402ceed22.RData new file mode 100644 index 000000000..4e9eb758a Binary files /dev/null and b/blogdown/en/sp/spr/gettingstarted_cache/html/cleaning_af88f1bc1bb0e2057ad9574402ceed22.RData differ diff --git a/content/en/sp/spr/steps_cache/html/construct_SYSargs2_trim-se_76dd283f4ac409fb76a14cdc8b0a1f66.rdb b/blogdown/en/sp/spr/gettingstarted_cache/html/cleaning_af88f1bc1bb0e2057ad9574402ceed22.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/construct_SYSargs2_trim-se_76dd283f4ac409fb76a14cdc8b0a1f66.rdb rename to blogdown/en/sp/spr/gettingstarted_cache/html/cleaning_af88f1bc1bb0e2057ad9574402ceed22.rdb diff --git a/content/en/sp/spr/steps_cache/html/construct_SYSargs2_trim-se_76dd283f4ac409fb76a14cdc8b0a1f66.rdx b/blogdown/en/sp/spr/gettingstarted_cache/html/cleaning_af88f1bc1bb0e2057ad9574402ceed22.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/construct_SYSargs2_trim-se_76dd283f4ac409fb76a14cdc8b0a1f66.rdx rename to blogdown/en/sp/spr/gettingstarted_cache/html/cleaning_af88f1bc1bb0e2057ad9574402ceed22.rdx diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/comment_lines_a751a89d87bb00e5f1af74a63fb49a1c.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/comment_lines_a751a89d87bb00e5f1af74a63fb49a1c.RData index 9d1d5eba4..5a742fb98 100644 Binary files a/blogdown/en/sp/spr/gettingstarted_cache/html/comment_lines_a751a89d87bb00e5f1af74a63fb49a1c.RData and b/blogdown/en/sp/spr/gettingstarted_cache/html/comment_lines_a751a89d87bb00e5f1af74a63fb49a1c.RData differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/dir_3f0833b061790677c6646f0fcb766916.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/dir_3f0833b061790677c6646f0fcb766916.RData deleted file mode 100644 index 9b74a8119..000000000 Binary files a/blogdown/en/sp/spr/gettingstarted_cache/html/dir_3f0833b061790677c6646f0fcb766916.RData and /dev/null differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/dir_d9f91c6228ae83cccffeb400a69bb949.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/dir_d9f91c6228ae83cccffeb400a69bb949.RData new file mode 100644 index 000000000..02a25db25 Binary files /dev/null and b/blogdown/en/sp/spr/gettingstarted_cache/html/dir_d9f91c6228ae83cccffeb400a69bb949.RData differ diff --git a/content/en/sp/spr/steps_cache/html/create_txdb_e52d7977be69727f22b38eae45736584.rdb b/blogdown/en/sp/spr/gettingstarted_cache/html/dir_d9f91c6228ae83cccffeb400a69bb949.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/create_txdb_e52d7977be69727f22b38eae45736584.rdb rename to blogdown/en/sp/spr/gettingstarted_cache/html/dir_d9f91c6228ae83cccffeb400a69bb949.rdb diff --git a/content/en/sp/spr/steps_cache/html/create_txdb_e52d7977be69727f22b38eae45736584.rdx b/blogdown/en/sp/spr/gettingstarted_cache/html/dir_d9f91c6228ae83cccffeb400a69bb949.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/create_txdb_e52d7977be69727f22b38eae45736584.rdx rename to blogdown/en/sp/spr/gettingstarted_cache/html/dir_d9f91c6228ae83cccffeb400a69bb949.rdx diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/documentation_108296e6faff1ad3205187446fd230ad.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/documentation_108296e6faff1ad3205187446fd230ad.RData new file mode 100644 index 000000000..a8b161557 Binary files /dev/null and b/blogdown/en/sp/spr/gettingstarted_cache/html/documentation_108296e6faff1ad3205187446fd230ad.RData differ diff --git a/content/en/sp/spr/steps_cache/html/custom_preprocessing_b01b3c1d8fb554e4ea67c8d2c506cac3.rdb b/blogdown/en/sp/spr/gettingstarted_cache/html/documentation_108296e6faff1ad3205187446fd230ad.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/custom_preprocessing_b01b3c1d8fb554e4ea67c8d2c506cac3.rdb rename to blogdown/en/sp/spr/gettingstarted_cache/html/documentation_108296e6faff1ad3205187446fd230ad.rdb diff --git a/content/en/sp/spr/steps_cache/html/custom_preprocessing_b01b3c1d8fb554e4ea67c8d2c506cac3.rdx b/blogdown/en/sp/spr/gettingstarted_cache/html/documentation_108296e6faff1ad3205187446fd230ad.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/custom_preprocessing_b01b3c1d8fb554e4ea67c8d2c506cac3.rdx rename to blogdown/en/sp/spr/gettingstarted_cache/html/documentation_108296e6faff1ad3205187446fd230ad.rdx diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/documentation_3369537b5da7730cafdc54b7e06bce1a.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/documentation_3369537b5da7730cafdc54b7e06bce1a.RData deleted file mode 100644 index 8f3fd9757..000000000 Binary files a/blogdown/en/sp/spr/gettingstarted_cache/html/documentation_3369537b5da7730cafdc54b7e06bce1a.RData and /dev/null differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/documentation_cf1d4843db726ce663b2bf916e2f450b.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/documentation_cf1d4843db726ce663b2bf916e2f450b.RData deleted file mode 100644 index f951b1a43..000000000 Binary files a/blogdown/en/sp/spr/gettingstarted_cache/html/documentation_cf1d4843db726ce663b2bf916e2f450b.RData and /dev/null differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/install_0ebfe8510aceb616bf6e78aee75d88e2.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/install_0ebfe8510aceb616bf6e78aee75d88e2.RData deleted file mode 100644 index bbf7a454c..000000000 Binary files a/blogdown/en/sp/spr/gettingstarted_cache/html/install_0ebfe8510aceb616bf6e78aee75d88e2.RData and /dev/null differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/install_7b263913cc8ee3c735574321403e08b8.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/install_7b263913cc8ee3c735574321403e08b8.RData deleted file mode 100644 index 0161d7914..000000000 Binary files a/blogdown/en/sp/spr/gettingstarted_cache/html/install_7b263913cc8ee3c735574321403e08b8.RData and /dev/null differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/install_deda95614c78b56fa13821d4a76a10a2.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/install_deda95614c78b56fa13821d4a76a10a2.RData new file mode 100644 index 000000000..3fa61a59b Binary files /dev/null and b/blogdown/en/sp/spr/gettingstarted_cache/html/install_deda95614c78b56fa13821d4a76a10a2.RData differ diff --git a/content/en/sp/spr/steps_cache/html/edger_deg_stats_e14bc959538ccf0771fd4fd76583fdf3.rdb b/blogdown/en/sp/spr/gettingstarted_cache/html/install_deda95614c78b56fa13821d4a76a10a2.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/edger_deg_stats_e14bc959538ccf0771fd4fd76583fdf3.rdb rename to blogdown/en/sp/spr/gettingstarted_cache/html/install_deda95614c78b56fa13821d4a76a10a2.rdb diff --git a/content/en/sp/spr/steps_cache/html/edger_deg_stats_e14bc959538ccf0771fd4fd76583fdf3.rdx b/blogdown/en/sp/spr/gettingstarted_cache/html/install_deda95614c78b56fa13821d4a76a10a2.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/edger_deg_stats_e14bc959538ccf0771fd4fd76583fdf3.rdx rename to blogdown/en/sp/spr/gettingstarted_cache/html/install_deda95614c78b56fa13821d4a76a10a2.rdx diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/setup_0791de71a9b1c983efd747e47ada9ceb.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/setup_0791de71a9b1c983efd747e47ada9ceb.RData new file mode 100644 index 000000000..1d12342af Binary files /dev/null and b/blogdown/en/sp/spr/gettingstarted_cache/html/setup_0791de71a9b1c983efd747e47ada9ceb.RData differ diff --git a/content/en/sp/spr/steps_cache/html/fastq_quality_41ee5fb48c2db6578f459be8ce9ccd0c.rdb b/blogdown/en/sp/spr/gettingstarted_cache/html/setup_0791de71a9b1c983efd747e47ada9ceb.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/fastq_quality_41ee5fb48c2db6578f459be8ce9ccd0c.rdb rename to blogdown/en/sp/spr/gettingstarted_cache/html/setup_0791de71a9b1c983efd747e47ada9ceb.rdb diff --git a/content/en/sp/spr/steps_cache/html/fastq_quality_41ee5fb48c2db6578f459be8ce9ccd0c.rdx b/blogdown/en/sp/spr/gettingstarted_cache/html/setup_0791de71a9b1c983efd747e47ada9ceb.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/fastq_quality_41ee5fb48c2db6578f459be8ce9ccd0c.rdx rename to blogdown/en/sp/spr/gettingstarted_cache/html/setup_0791de71a9b1c983efd747e47ada9ceb.rdx diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/setup_364d4b0afd20170202ebe6c445f9700f.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/setup_364d4b0afd20170202ebe6c445f9700f.RData deleted file mode 100644 index f3c1ca180..000000000 Binary files a/blogdown/en/sp/spr/gettingstarted_cache/html/setup_364d4b0afd20170202ebe6c445f9700f.RData and /dev/null differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/setup_b2105ac0d2ccba413cf8eafdb5073f26.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/setup_b2105ac0d2ccba413cf8eafdb5073f26.RData deleted file mode 100644 index 374bd8302..000000000 Binary files a/blogdown/en/sp/spr/gettingstarted_cache/html/setup_b2105ac0d2ccba413cf8eafdb5073f26.RData and /dev/null differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsFig_4012986a1ec65274e17a3eb3f36661a7.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsFig_4012986a1ec65274e17a3eb3f36661a7.RData new file mode 100644 index 000000000..0fd911d1e Binary files /dev/null and b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsFig_4012986a1ec65274e17a3eb3f36661a7.RData differ diff --git a/content/en/sp/spr/steps_cache/html/fastq_quality_parallel_cluster_49f0d1290e28b1bf7cf8daf58c4e4064.rdb b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsFig_4012986a1ec65274e17a3eb3f36661a7.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/fastq_quality_parallel_cluster_49f0d1290e28b1bf7cf8daf58c4e4064.rdb rename to blogdown/en/sp/spr/gettingstarted_cache/html/targetsFig_4012986a1ec65274e17a3eb3f36661a7.rdb diff --git a/content/en/sp/spr/steps_cache/html/fastq_quality_parallel_cluster_49f0d1290e28b1bf7cf8daf58c4e4064.rdx b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsFig_4012986a1ec65274e17a3eb3f36661a7.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/fastq_quality_parallel_cluster_49f0d1290e28b1bf7cf8daf58c4e4064.rdx rename to blogdown/en/sp/spr/gettingstarted_cache/html/targetsFig_4012986a1ec65274e17a3eb3f36661a7.rdx diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsFig_5c9371815426b7b2e17a029843a1690b.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsFig_5c9371815426b7b2e17a029843a1690b.RData deleted file mode 100644 index c4c57df34..000000000 Binary files a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsFig_5c9371815426b7b2e17a029843a1690b.RData and /dev/null differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsPE_876f242ada989683e2dff3045126207e.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsPE_876f242ada989683e2dff3045126207e.RData deleted file mode 100644 index 5455b9f3f..000000000 Binary files a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsPE_876f242ada989683e2dff3045126207e.RData and /dev/null differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsPE_876f242ada989683e2dff3045126207e.rdb b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsPE_876f242ada989683e2dff3045126207e.rdb deleted file mode 100644 index 3a8b22621..000000000 Binary files a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsPE_876f242ada989683e2dff3045126207e.rdb and /dev/null differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsPE_876f242ada989683e2dff3045126207e.rdx b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsPE_876f242ada989683e2dff3045126207e.rdx deleted file mode 100644 index 32714e45e..000000000 Binary files a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsPE_876f242ada989683e2dff3045126207e.rdx and /dev/null differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsPE_9e629ff07f8f09da5e18cec03dcbd90e.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsPE_9e629ff07f8f09da5e18cec03dcbd90e.RData new file mode 100644 index 000000000..e37ed0962 Binary files /dev/null and b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsPE_9e629ff07f8f09da5e18cec03dcbd90e.RData differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsPE_9e629ff07f8f09da5e18cec03dcbd90e.rdb b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsPE_9e629ff07f8f09da5e18cec03dcbd90e.rdb new file mode 100644 index 000000000..5bddec2f0 Binary files /dev/null and b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsPE_9e629ff07f8f09da5e18cec03dcbd90e.rdb differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsPE_9e629ff07f8f09da5e18cec03dcbd90e.rdx b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsPE_9e629ff07f8f09da5e18cec03dcbd90e.rdx new file mode 100644 index 000000000..8cc364377 Binary files /dev/null and b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsPE_9e629ff07f8f09da5e18cec03dcbd90e.rdx differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsSE_0f0d8e9ecd132a6c5a9f4a50776e1de0.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsSE_0f0d8e9ecd132a6c5a9f4a50776e1de0.RData deleted file mode 100644 index cfc9164e0..000000000 Binary files a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsSE_0f0d8e9ecd132a6c5a9f4a50776e1de0.RData and /dev/null differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsSE_0f0d8e9ecd132a6c5a9f4a50776e1de0.rdb b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsSE_0f0d8e9ecd132a6c5a9f4a50776e1de0.rdb deleted file mode 100644 index bbf65191d..000000000 Binary files a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsSE_0f0d8e9ecd132a6c5a9f4a50776e1de0.rdb and /dev/null differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsSE_0f0d8e9ecd132a6c5a9f4a50776e1de0.rdx b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsSE_0f0d8e9ecd132a6c5a9f4a50776e1de0.rdx deleted file mode 100644 index 0a2b0e7e1..000000000 Binary files a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsSE_0f0d8e9ecd132a6c5a9f4a50776e1de0.rdx and /dev/null differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsSE_2c23d1d347f9a7bad3cf2c2ab93336a6.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsSE_2c23d1d347f9a7bad3cf2c2ab93336a6.RData new file mode 100644 index 000000000..9fb369786 Binary files /dev/null and b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsSE_2c23d1d347f9a7bad3cf2c2ab93336a6.RData differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsSE_2c23d1d347f9a7bad3cf2c2ab93336a6.rdb b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsSE_2c23d1d347f9a7bad3cf2c2ab93336a6.rdb new file mode 100644 index 000000000..1d45b91cd Binary files /dev/null and b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsSE_2c23d1d347f9a7bad3cf2c2ab93336a6.rdb differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsSE_2c23d1d347f9a7bad3cf2c2ab93336a6.rdx b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsSE_2c23d1d347f9a7bad3cf2c2ab93336a6.rdx new file mode 100644 index 000000000..5cf2cb8c5 Binary files /dev/null and b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsSE_2c23d1d347f9a7bad3cf2c2ab93336a6.rdx differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targets_echo_41cd78bb9c41eb6afff6e76a658b31aa.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/targets_echo_41cd78bb9c41eb6afff6e76a658b31aa.RData deleted file mode 100644 index 44afc7912..000000000 Binary files a/blogdown/en/sp/spr/gettingstarted_cache/html/targets_echo_41cd78bb9c41eb6afff6e76a658b31aa.RData and /dev/null differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targets_echo_41cd78bb9c41eb6afff6e76a658b31aa.rdb b/blogdown/en/sp/spr/gettingstarted_cache/html/targets_echo_41cd78bb9c41eb6afff6e76a658b31aa.rdb deleted file mode 100644 index bd42277e7..000000000 Binary files a/blogdown/en/sp/spr/gettingstarted_cache/html/targets_echo_41cd78bb9c41eb6afff6e76a658b31aa.rdb and /dev/null differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targets_echo_41cd78bb9c41eb6afff6e76a658b31aa.rdx b/blogdown/en/sp/spr/gettingstarted_cache/html/targets_echo_41cd78bb9c41eb6afff6e76a658b31aa.rdx deleted file mode 100644 index 915a2ed8d..000000000 Binary files a/blogdown/en/sp/spr/gettingstarted_cache/html/targets_echo_41cd78bb9c41eb6afff6e76a658b31aa.rdx and /dev/null differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targets_echo_5df2e9f765638460a19da30048dd2671.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/targets_echo_5df2e9f765638460a19da30048dd2671.RData new file mode 100644 index 000000000..2c9026c40 Binary files /dev/null and b/blogdown/en/sp/spr/gettingstarted_cache/html/targets_echo_5df2e9f765638460a19da30048dd2671.RData differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targets_echo_5df2e9f765638460a19da30048dd2671.rdb b/blogdown/en/sp/spr/gettingstarted_cache/html/targets_echo_5df2e9f765638460a19da30048dd2671.rdb new file mode 100644 index 000000000..d30825b69 Binary files /dev/null and b/blogdown/en/sp/spr/gettingstarted_cache/html/targets_echo_5df2e9f765638460a19da30048dd2671.rdb differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targets_echo_5df2e9f765638460a19da30048dd2671.rdx b/blogdown/en/sp/spr/gettingstarted_cache/html/targets_echo_5df2e9f765638460a19da30048dd2671.rdx new file mode 100644 index 000000000..3c881df81 Binary files /dev/null and b/blogdown/en/sp/spr/gettingstarted_cache/html/targets_echo_5df2e9f765638460a19da30048dd2671.rdx differ diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetscomp_79d62d33ebd81a0807bd482b7bdd7768.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/targetscomp_79d62d33ebd81a0807bd482b7bdd7768.RData new file mode 100644 index 000000000..3b57554e9 Binary files /dev/null and b/blogdown/en/sp/spr/gettingstarted_cache/html/targetscomp_79d62d33ebd81a0807bd482b7bdd7768.RData differ diff --git a/content/en/sp/spr/steps_cache/html/fastq_quality_parallel_single_5b1564106f2b840be6480447b9cd5d70.rdb b/blogdown/en/sp/spr/gettingstarted_cache/html/targetscomp_79d62d33ebd81a0807bd482b7bdd7768.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/fastq_quality_parallel_single_5b1564106f2b840be6480447b9cd5d70.rdb rename to blogdown/en/sp/spr/gettingstarted_cache/html/targetscomp_79d62d33ebd81a0807bd482b7bdd7768.rdb diff --git a/content/en/sp/spr/steps_cache/html/fastq_quality_parallel_single_5b1564106f2b840be6480447b9cd5d70.rdx b/blogdown/en/sp/spr/gettingstarted_cache/html/targetscomp_79d62d33ebd81a0807bd482b7bdd7768.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/fastq_quality_parallel_single_5b1564106f2b840be6480447b9cd5d70.rdx rename to blogdown/en/sp/spr/gettingstarted_cache/html/targetscomp_79d62d33ebd81a0807bd482b7bdd7768.rdx diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetscomp_a16aec4247ee217dbaf82f15ba34e9d0.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/targetscomp_a16aec4247ee217dbaf82f15ba34e9d0.RData deleted file mode 100644 index 702ef48f0..000000000 Binary files a/blogdown/en/sp/spr/gettingstarted_cache/html/targetscomp_a16aec4247ee217dbaf82f15ba34e9d0.RData and /dev/null differ diff --git a/content/en/sp/spr/steps_cache/html/__packages b/blogdown/en/sp/spr/steps_cache/html/__packages similarity index 100% rename from content/en/sp/spr/steps_cache/html/__packages rename to blogdown/en/sp/spr/steps_cache/html/__packages diff --git a/blogdown/en/sp/spr/steps_cache/html/align_stats1_bbed94d6c92615d94d5d3f175e681c09.RData b/blogdown/en/sp/spr/steps_cache/html/align_stats1_bbed94d6c92615d94d5d3f175e681c09.RData new file mode 100644 index 000000000..00808df36 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/align_stats1_bbed94d6c92615d94d5d3f175e681c09.RData differ diff --git a/content/en/sp/spr/steps_cache/html/get_go_biomart_4dc593b5439f1dec6fcfd43518db4beb.rdb b/blogdown/en/sp/spr/steps_cache/html/align_stats1_bbed94d6c92615d94d5d3f175e681c09.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/get_go_biomart_4dc593b5439f1dec6fcfd43518db4beb.rdb rename to blogdown/en/sp/spr/steps_cache/html/align_stats1_bbed94d6c92615d94d5d3f175e681c09.rdb diff --git a/content/en/sp/spr/steps_cache/html/get_go_biomart_4dc593b5439f1dec6fcfd43518db4beb.rdx b/blogdown/en/sp/spr/steps_cache/html/align_stats1_bbed94d6c92615d94d5d3f175e681c09.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/get_go_biomart_4dc593b5439f1dec6fcfd43518db4beb.rdx rename to blogdown/en/sp/spr/steps_cache/html/align_stats1_bbed94d6c92615d94d5d3f175e681c09.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/align_stats2_f22d201c8f92ffb5670975c1ff8dd45f.RData b/blogdown/en/sp/spr/steps_cache/html/align_stats2_f22d201c8f92ffb5670975c1ff8dd45f.RData new file mode 100644 index 000000000..c8c5aab53 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/align_stats2_f22d201c8f92ffb5670975c1ff8dd45f.RData differ diff --git a/content/en/sp/spr/steps_cache/html/go_enrichment_35387ce89176d3f0e4f98b66acca148f.rdb b/blogdown/en/sp/spr/steps_cache/html/align_stats2_f22d201c8f92ffb5670975c1ff8dd45f.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/go_enrichment_35387ce89176d3f0e4f98b66acca148f.rdb rename to blogdown/en/sp/spr/steps_cache/html/align_stats2_f22d201c8f92ffb5670975c1ff8dd45f.rdb diff --git a/content/en/sp/spr/steps_cache/html/go_enrichment_35387ce89176d3f0e4f98b66acca148f.rdx b/blogdown/en/sp/spr/steps_cache/html/align_stats2_f22d201c8f92ffb5670975c1ff8dd45f.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/go_enrichment_35387ce89176d3f0e4f98b66acca148f.rdx rename to blogdown/en/sp/spr/steps_cache/html/align_stats2_f22d201c8f92ffb5670975c1ff8dd45f.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/align_stats_parallel_cluster_086068d906c9258c3ce3f182b66b95a8.RData b/blogdown/en/sp/spr/steps_cache/html/align_stats_parallel_cluster_086068d906c9258c3ce3f182b66b95a8.RData new file mode 100644 index 000000000..883023561 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/align_stats_parallel_cluster_086068d906c9258c3ce3f182b66b95a8.RData differ diff --git a/content/en/sp/spr/steps_cache/html/gsnap_89ae5ce91c3357980d46051cad056c24.rdb b/blogdown/en/sp/spr/steps_cache/html/align_stats_parallel_cluster_086068d906c9258c3ce3f182b66b95a8.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/gsnap_89ae5ce91c3357980d46051cad056c24.rdb rename to blogdown/en/sp/spr/steps_cache/html/align_stats_parallel_cluster_086068d906c9258c3ce3f182b66b95a8.rdb diff --git a/content/en/sp/spr/steps_cache/html/gsnap_89ae5ce91c3357980d46051cad056c24.rdx b/blogdown/en/sp/spr/steps_cache/html/align_stats_parallel_cluster_086068d906c9258c3ce3f182b66b95a8.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/gsnap_89ae5ce91c3357980d46051cad056c24.rdx rename to blogdown/en/sp/spr/steps_cache/html/align_stats_parallel_cluster_086068d906c9258c3ce3f182b66b95a8.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/align_stats_parallel_e979f127f5223d5a7a6264536e6c117c.RData b/blogdown/en/sp/spr/steps_cache/html/align_stats_parallel_e979f127f5223d5a7a6264536e6c117c.RData new file mode 100644 index 000000000..bf9893e60 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/align_stats_parallel_e979f127f5223d5a7a6264536e6c117c.RData differ diff --git a/content/en/sp/spr/steps_cache/html/hierarchical_clustering_05d3ce56f6243ea7b6e6ec456a5ca350.rdb b/blogdown/en/sp/spr/steps_cache/html/align_stats_parallel_e979f127f5223d5a7a6264536e6c117c.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/hierarchical_clustering_05d3ce56f6243ea7b6e6ec456a5ca350.rdb rename to blogdown/en/sp/spr/steps_cache/html/align_stats_parallel_e979f127f5223d5a7a6264536e6c117c.rdb diff --git a/content/en/sp/spr/steps_cache/html/hierarchical_clustering_05d3ce56f6243ea7b6e6ec456a5ca350.rdx b/blogdown/en/sp/spr/steps_cache/html/align_stats_parallel_e979f127f5223d5a7a6264536e6c117c.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/hierarchical_clustering_05d3ce56f6243ea7b6e6ec456a5ca350.rdx rename to blogdown/en/sp/spr/steps_cache/html/align_stats_parallel_e979f127f5223d5a7a6264536e6c117c.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/bowtie2_SYSargs2_0ba1c929e47af08723bdbef9dcaa06f5.RData b/blogdown/en/sp/spr/steps_cache/html/bowtie2_SYSargs2_0ba1c929e47af08723bdbef9dcaa06f5.RData new file mode 100644 index 000000000..68534d1da Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/bowtie2_SYSargs2_0ba1c929e47af08723bdbef9dcaa06f5.RData differ diff --git a/content/en/sp/spr/steps_cache/html/hisat_alignment_e669aa8f2ed56a267110172c4013bce1.rdb b/blogdown/en/sp/spr/steps_cache/html/bowtie2_SYSargs2_0ba1c929e47af08723bdbef9dcaa06f5.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/hisat_alignment_e669aa8f2ed56a267110172c4013bce1.rdb rename to blogdown/en/sp/spr/steps_cache/html/bowtie2_SYSargs2_0ba1c929e47af08723bdbef9dcaa06f5.rdb diff --git a/content/en/sp/spr/steps_cache/html/hisat_alignment_e669aa8f2ed56a267110172c4013bce1.rdx b/blogdown/en/sp/spr/steps_cache/html/bowtie2_SYSargs2_0ba1c929e47af08723bdbef9dcaa06f5.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/hisat_alignment_e669aa8f2ed56a267110172c4013bce1.rdx rename to blogdown/en/sp/spr/steps_cache/html/bowtie2_SYSargs2_0ba1c929e47af08723bdbef9dcaa06f5.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/bowtie2_cluster_84541c2641463ee0551ec93af01350c7.RData b/blogdown/en/sp/spr/steps_cache/html/bowtie2_cluster_84541c2641463ee0551ec93af01350c7.RData new file mode 100644 index 000000000..387c5c1f5 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/bowtie2_cluster_84541c2641463ee0551ec93af01350c7.RData differ diff --git a/content/en/sp/spr/steps_cache/html/hisat_index_25d74645d1f7b27eb56822ad36381b7b.rdb b/blogdown/en/sp/spr/steps_cache/html/bowtie2_cluster_84541c2641463ee0551ec93af01350c7.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/hisat_index_25d74645d1f7b27eb56822ad36381b7b.rdb rename to blogdown/en/sp/spr/steps_cache/html/bowtie2_cluster_84541c2641463ee0551ec93af01350c7.rdb diff --git a/content/en/sp/spr/steps_cache/html/hisat_index_25d74645d1f7b27eb56822ad36381b7b.rdx b/blogdown/en/sp/spr/steps_cache/html/bowtie2_cluster_84541c2641463ee0551ec93af01350c7.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/hisat_index_25d74645d1f7b27eb56822ad36381b7b.rdx rename to blogdown/en/sp/spr/steps_cache/html/bowtie2_cluster_84541c2641463ee0551ec93af01350c7.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/bowtie2_index_8382c5228cd478f2ba6ab0e21a013b3d.RData b/blogdown/en/sp/spr/steps_cache/html/bowtie2_index_8382c5228cd478f2ba6ab0e21a013b3d.RData new file mode 100644 index 000000000..7b172a4c5 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/bowtie2_index_8382c5228cd478f2ba6ab0e21a013b3d.RData differ diff --git a/content/en/sp/spr/steps_cache/html/igv_ece3317146f7e7ed97ce2d0de59851e1.rdb b/blogdown/en/sp/spr/steps_cache/html/bowtie2_index_8382c5228cd478f2ba6ab0e21a013b3d.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/igv_ece3317146f7e7ed97ce2d0de59851e1.rdb rename to blogdown/en/sp/spr/steps_cache/html/bowtie2_index_8382c5228cd478f2ba6ab0e21a013b3d.rdb diff --git a/content/en/sp/spr/steps_cache/html/igv_ece3317146f7e7ed97ce2d0de59851e1.rdx b/blogdown/en/sp/spr/steps_cache/html/bowtie2_index_8382c5228cd478f2ba6ab0e21a013b3d.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/igv_ece3317146f7e7ed97ce2d0de59851e1.rdx rename to blogdown/en/sp/spr/steps_cache/html/bowtie2_index_8382c5228cd478f2ba6ab0e21a013b3d.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/bowtie2_sm_b18a741dd5326898fa27fea0f9d1cc84.RData b/blogdown/en/sp/spr/steps_cache/html/bowtie2_sm_b18a741dd5326898fa27fea0f9d1cc84.RData new file mode 100644 index 000000000..1cdcc79d4 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/bowtie2_sm_b18a741dd5326898fa27fea0f9d1cc84.RData differ diff --git a/content/en/sp/spr/steps_cache/html/load_package_6f6a70fd05972b085fe84dd1bd54ac76.rdb b/blogdown/en/sp/spr/steps_cache/html/bowtie2_sm_b18a741dd5326898fa27fea0f9d1cc84.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/load_package_6f6a70fd05972b085fe84dd1bd54ac76.rdb rename to blogdown/en/sp/spr/steps_cache/html/bowtie2_sm_b18a741dd5326898fa27fea0f9d1cc84.rdb diff --git a/content/en/sp/spr/steps_cache/html/load_package_6f6a70fd05972b085fe84dd1bd54ac76.rdx b/blogdown/en/sp/spr/steps_cache/html/bowtie2_sm_b18a741dd5326898fa27fea0f9d1cc84.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/load_package_6f6a70fd05972b085fe84dd1bd54ac76.rdx rename to blogdown/en/sp/spr/steps_cache/html/bowtie2_sm_b18a741dd5326898fa27fea0f9d1cc84.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/bowtie_index_394fac0e0b547f4c75bde11c859ff908.RData b/blogdown/en/sp/spr/steps_cache/html/bowtie_index_394fac0e0b547f4c75bde11c859ff908.RData new file mode 100644 index 000000000..0e813c87d Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/bowtie_index_394fac0e0b547f4c75bde11c859ff908.RData differ diff --git a/content/en/sp/spr/steps_cache/html/output_865596eb82456661421f2c6f4e555b0a.rdb b/blogdown/en/sp/spr/steps_cache/html/bowtie_index_394fac0e0b547f4c75bde11c859ff908.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/output_865596eb82456661421f2c6f4e555b0a.rdb rename to blogdown/en/sp/spr/steps_cache/html/bowtie_index_394fac0e0b547f4c75bde11c859ff908.rdb diff --git a/content/en/sp/spr/steps_cache/html/output_865596eb82456661421f2c6f4e555b0a.rdx b/blogdown/en/sp/spr/steps_cache/html/bowtie_index_394fac0e0b547f4c75bde11c859ff908.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/output_865596eb82456661421f2c6f4e555b0a.rdx rename to blogdown/en/sp/spr/steps_cache/html/bowtie_index_394fac0e0b547f4c75bde11c859ff908.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/bwa-pe_alignment_e03c6c80578d0fbed2bef40b5f062b07.RData b/blogdown/en/sp/spr/steps_cache/html/bwa-pe_alignment_e03c6c80578d0fbed2bef40b5f062b07.RData new file mode 100644 index 000000000..99924e963 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/bwa-pe_alignment_e03c6c80578d0fbed2bef40b5f062b07.RData differ diff --git a/content/en/sp/spr/steps_cache/html/plot_go_enrichment_833c2c54a3520f2b1070d876a70dec01.rdb b/blogdown/en/sp/spr/steps_cache/html/bwa-pe_alignment_e03c6c80578d0fbed2bef40b5f062b07.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/plot_go_enrichment_833c2c54a3520f2b1070d876a70dec01.rdb rename to blogdown/en/sp/spr/steps_cache/html/bwa-pe_alignment_e03c6c80578d0fbed2bef40b5f062b07.rdb diff --git a/content/en/sp/spr/steps_cache/html/plot_go_enrichment_833c2c54a3520f2b1070d876a70dec01.rdx b/blogdown/en/sp/spr/steps_cache/html/bwa-pe_alignment_e03c6c80578d0fbed2bef40b5f062b07.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/plot_go_enrichment_833c2c54a3520f2b1070d876a70dec01.rdx rename to blogdown/en/sp/spr/steps_cache/html/bwa-pe_alignment_e03c6c80578d0fbed2bef40b5f062b07.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/bwa_index_745e218536bf605c1bac0002d3baf091.RData b/blogdown/en/sp/spr/steps_cache/html/bwa_index_745e218536bf605c1bac0002d3baf091.RData new file mode 100644 index 000000000..330d9a3a2 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/bwa_index_745e218536bf605c1bac0002d3baf091.RData differ diff --git a/content/en/sp/spr/steps_cache/html/preprocessing_56b1b4000496862fe9f3bceb787719a5.rdb b/blogdown/en/sp/spr/steps_cache/html/bwa_index_745e218536bf605c1bac0002d3baf091.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/preprocessing_56b1b4000496862fe9f3bceb787719a5.rdb rename to blogdown/en/sp/spr/steps_cache/html/bwa_index_745e218536bf605c1bac0002d3baf091.rdb diff --git a/content/en/sp/spr/steps_cache/html/preprocessing_56b1b4000496862fe9f3bceb787719a5.rdx b/blogdown/en/sp/spr/steps_cache/html/bwa_index_745e218536bf605c1bac0002d3baf091.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/preprocessing_56b1b4000496862fe9f3bceb787719a5.rdx rename to blogdown/en/sp/spr/steps_cache/html/bwa_index_745e218536bf605c1bac0002d3baf091.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/clusterRun_args_79c841a002a5de4486783c2c3c31d530.RData b/blogdown/en/sp/spr/steps_cache/html/clusterRun_args_79c841a002a5de4486783c2c3c31d530.RData new file mode 100644 index 000000000..e62650752 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/clusterRun_args_79c841a002a5de4486783c2c3c31d530.RData differ diff --git a/content/en/sp/spr/steps_cache/html/process_monitoring_2e6e25d17bd7df07433846378baa2936.rdb b/blogdown/en/sp/spr/steps_cache/html/clusterRun_args_79c841a002a5de4486783c2c3c31d530.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/process_monitoring_2e6e25d17bd7df07433846378baa2936.rdb rename to blogdown/en/sp/spr/steps_cache/html/clusterRun_args_79c841a002a5de4486783c2c3c31d530.rdb diff --git a/content/en/sp/spr/steps_cache/html/process_monitoring_2e6e25d17bd7df07433846378baa2936.rdx b/blogdown/en/sp/spr/steps_cache/html/clusterRun_args_79c841a002a5de4486783c2c3c31d530.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/process_monitoring_2e6e25d17bd7df07433846378baa2936.rdx rename to blogdown/en/sp/spr/steps_cache/html/clusterRun_args_79c841a002a5de4486783c2c3c31d530.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/construct_SYSargs2_trim-pe_158bfd8b75e929f8c402a13f131e5dd2.RData b/blogdown/en/sp/spr/steps_cache/html/construct_SYSargs2_trim-pe_158bfd8b75e929f8c402a13f131e5dd2.RData new file mode 100644 index 000000000..654b891c8 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/construct_SYSargs2_trim-pe_158bfd8b75e929f8c402a13f131e5dd2.RData differ diff --git a/content/en/sp/spr/steps_cache/html/read_counting_mirna_66b5a07a5be94ab1e2f670cec2fc67fd.rdb b/blogdown/en/sp/spr/steps_cache/html/construct_SYSargs2_trim-pe_158bfd8b75e929f8c402a13f131e5dd2.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/read_counting_mirna_66b5a07a5be94ab1e2f670cec2fc67fd.rdb rename to blogdown/en/sp/spr/steps_cache/html/construct_SYSargs2_trim-pe_158bfd8b75e929f8c402a13f131e5dd2.rdb diff --git a/content/en/sp/spr/steps_cache/html/read_counting_mirna_66b5a07a5be94ab1e2f670cec2fc67fd.rdx b/blogdown/en/sp/spr/steps_cache/html/construct_SYSargs2_trim-pe_158bfd8b75e929f8c402a13f131e5dd2.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/read_counting_mirna_66b5a07a5be94ab1e2f670cec2fc67fd.rdx rename to blogdown/en/sp/spr/steps_cache/html/construct_SYSargs2_trim-pe_158bfd8b75e929f8c402a13f131e5dd2.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/construct_SYSargs2_trim-se_8b5ebda9947aba81a017f76a7779eb82.RData b/blogdown/en/sp/spr/steps_cache/html/construct_SYSargs2_trim-se_8b5ebda9947aba81a017f76a7779eb82.RData new file mode 100644 index 000000000..d38b73adf Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/construct_SYSargs2_trim-se_8b5ebda9947aba81a017f76a7779eb82.RData differ diff --git a/content/en/sp/spr/steps_cache/html/read_counting_multicore_41871f98000ea684a2e2cda2cdde5a81.rdb b/blogdown/en/sp/spr/steps_cache/html/construct_SYSargs2_trim-se_8b5ebda9947aba81a017f76a7779eb82.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/read_counting_multicore_41871f98000ea684a2e2cda2cdde5a81.rdb rename to blogdown/en/sp/spr/steps_cache/html/construct_SYSargs2_trim-se_8b5ebda9947aba81a017f76a7779eb82.rdb diff --git a/content/en/sp/spr/steps_cache/html/read_counting_multicore_41871f98000ea684a2e2cda2cdde5a81.rdx b/blogdown/en/sp/spr/steps_cache/html/construct_SYSargs2_trim-se_8b5ebda9947aba81a017f76a7779eb82.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/read_counting_multicore_41871f98000ea684a2e2cda2cdde5a81.rdx rename to blogdown/en/sp/spr/steps_cache/html/construct_SYSargs2_trim-se_8b5ebda9947aba81a017f76a7779eb82.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/create_txdb_e4df674f257dbf4b02caf293e331b31e.RData b/blogdown/en/sp/spr/steps_cache/html/create_txdb_e4df674f257dbf4b02caf293e331b31e.RData new file mode 100644 index 000000000..ceeb72752 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/create_txdb_e4df674f257dbf4b02caf293e331b31e.RData differ diff --git a/content/en/sp/spr/steps_cache/html/read_counting_multinode_03a1e0fc570dbee395c0fed986f615f0.rdb b/blogdown/en/sp/spr/steps_cache/html/create_txdb_e4df674f257dbf4b02caf293e331b31e.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/read_counting_multinode_03a1e0fc570dbee395c0fed986f615f0.rdb rename to blogdown/en/sp/spr/steps_cache/html/create_txdb_e4df674f257dbf4b02caf293e331b31e.rdb diff --git a/content/en/sp/spr/steps_cache/html/read_counting_multinode_03a1e0fc570dbee395c0fed986f615f0.rdx b/blogdown/en/sp/spr/steps_cache/html/create_txdb_e4df674f257dbf4b02caf293e331b31e.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/read_counting_multinode_03a1e0fc570dbee395c0fed986f615f0.rdx rename to blogdown/en/sp/spr/steps_cache/html/create_txdb_e4df674f257dbf4b02caf293e331b31e.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/custom_preprocessing_cbfb8462495e4f2be1a150bf301deae0.RData b/blogdown/en/sp/spr/steps_cache/html/custom_preprocessing_cbfb8462495e4f2be1a150bf301deae0.RData new file mode 100644 index 000000000..f3397d483 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/custom_preprocessing_cbfb8462495e4f2be1a150bf301deae0.RData differ diff --git a/content/en/sp/spr/steps_cache/html/rsubread_1ac9c4d5dc0336480fc5e5de040febb9.rdb b/blogdown/en/sp/spr/steps_cache/html/custom_preprocessing_cbfb8462495e4f2be1a150bf301deae0.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/rsubread_1ac9c4d5dc0336480fc5e5de040febb9.rdb rename to blogdown/en/sp/spr/steps_cache/html/custom_preprocessing_cbfb8462495e4f2be1a150bf301deae0.rdb diff --git a/content/en/sp/spr/steps_cache/html/rsubread_1ac9c4d5dc0336480fc5e5de040febb9.rdx b/blogdown/en/sp/spr/steps_cache/html/custom_preprocessing_cbfb8462495e4f2be1a150bf301deae0.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/rsubread_1ac9c4d5dc0336480fc5e5de040febb9.rdx rename to blogdown/en/sp/spr/steps_cache/html/custom_preprocessing_cbfb8462495e4f2be1a150bf301deae0.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/deseq2_deg_counts_26dc89b184693371049e7082d894b2a1.RData b/blogdown/en/sp/spr/steps_cache/html/deseq2_deg_counts_26dc89b184693371049e7082d894b2a1.RData new file mode 100644 index 000000000..b451d8364 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/deseq2_deg_counts_26dc89b184693371049e7082d894b2a1.RData differ diff --git a/content/en/sp/spr/steps_cache/html/deseq2_deg_counts_486957f565e99d9ddc5a6e45d7683ded.rdb b/blogdown/en/sp/spr/steps_cache/html/deseq2_deg_counts_26dc89b184693371049e7082d894b2a1.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/deseq2_deg_counts_486957f565e99d9ddc5a6e45d7683ded.rdb rename to blogdown/en/sp/spr/steps_cache/html/deseq2_deg_counts_26dc89b184693371049e7082d894b2a1.rdb diff --git a/content/en/sp/spr/steps_cache/html/deseq2_deg_counts_486957f565e99d9ddc5a6e45d7683ded.rdx b/blogdown/en/sp/spr/steps_cache/html/deseq2_deg_counts_26dc89b184693371049e7082d894b2a1.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/deseq2_deg_counts_486957f565e99d9ddc5a6e45d7683ded.rdx rename to blogdown/en/sp/spr/steps_cache/html/deseq2_deg_counts_26dc89b184693371049e7082d894b2a1.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/deseq2_wrapper_9f0ac28bd96218989eff50345fdc6460.RData b/blogdown/en/sp/spr/steps_cache/html/deseq2_wrapper_9f0ac28bd96218989eff50345fdc6460.RData new file mode 100644 index 000000000..a7b06bebf Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/deseq2_wrapper_9f0ac28bd96218989eff50345fdc6460.RData differ diff --git a/content/en/sp/spr/steps_cache/html/deseq2_wrapper_bc871c74bafc63343820156ac0c8fc0c.rdb b/blogdown/en/sp/spr/steps_cache/html/deseq2_wrapper_9f0ac28bd96218989eff50345fdc6460.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/deseq2_wrapper_bc871c74bafc63343820156ac0c8fc0c.rdb rename to blogdown/en/sp/spr/steps_cache/html/deseq2_wrapper_9f0ac28bd96218989eff50345fdc6460.rdb diff --git a/content/en/sp/spr/steps_cache/html/deseq2_wrapper_bc871c74bafc63343820156ac0c8fc0c.rdx b/blogdown/en/sp/spr/steps_cache/html/deseq2_wrapper_9f0ac28bd96218989eff50345fdc6460.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/deseq2_wrapper_bc871c74bafc63343820156ac0c8fc0c.rdx rename to blogdown/en/sp/spr/steps_cache/html/deseq2_wrapper_9f0ac28bd96218989eff50345fdc6460.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/edger_deg_counts_cc09379f2c605cdf8f43fafdb766ddf6.RData b/blogdown/en/sp/spr/steps_cache/html/edger_deg_counts_cc09379f2c605cdf8f43fafdb766ddf6.RData new file mode 100644 index 000000000..22a75f46b Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/edger_deg_counts_cc09379f2c605cdf8f43fafdb766ddf6.RData differ diff --git a/content/en/sp/spr/steps_cache/html/edger_deg_counts_4b283f3f029939b2d9ca463b6ebc5bdc.rdb b/blogdown/en/sp/spr/steps_cache/html/edger_deg_counts_cc09379f2c605cdf8f43fafdb766ddf6.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/edger_deg_counts_4b283f3f029939b2d9ca463b6ebc5bdc.rdb rename to blogdown/en/sp/spr/steps_cache/html/edger_deg_counts_cc09379f2c605cdf8f43fafdb766ddf6.rdb diff --git a/content/en/sp/spr/steps_cache/html/edger_deg_counts_4b283f3f029939b2d9ca463b6ebc5bdc.rdx b/blogdown/en/sp/spr/steps_cache/html/edger_deg_counts_cc09379f2c605cdf8f43fafdb766ddf6.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/edger_deg_counts_4b283f3f029939b2d9ca463b6ebc5bdc.rdx rename to blogdown/en/sp/spr/steps_cache/html/edger_deg_counts_cc09379f2c605cdf8f43fafdb766ddf6.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/edger_deg_stats_174f0af974b06e7eef9cdf3cc03c85b9.RData b/blogdown/en/sp/spr/steps_cache/html/edger_deg_stats_174f0af974b06e7eef9cdf3cc03c85b9.RData new file mode 100644 index 000000000..52b4c5896 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/edger_deg_stats_174f0af974b06e7eef9cdf3cc03c85b9.RData differ diff --git a/content/en/sp/spr/steps_cache/html/runCommandline_align_35bd45e3201e14ca6e386f36a01b3e2b.rdb b/blogdown/en/sp/spr/steps_cache/html/edger_deg_stats_174f0af974b06e7eef9cdf3cc03c85b9.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/runCommandline_align_35bd45e3201e14ca6e386f36a01b3e2b.rdb rename to blogdown/en/sp/spr/steps_cache/html/edger_deg_stats_174f0af974b06e7eef9cdf3cc03c85b9.rdb diff --git a/content/en/sp/spr/steps_cache/html/runCommandline_align_35bd45e3201e14ca6e386f36a01b3e2b.rdx b/blogdown/en/sp/spr/steps_cache/html/edger_deg_stats_174f0af974b06e7eef9cdf3cc03c85b9.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/runCommandline_align_35bd45e3201e14ca6e386f36a01b3e2b.rdx rename to blogdown/en/sp/spr/steps_cache/html/edger_deg_stats_174f0af974b06e7eef9cdf3cc03c85b9.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/edger_wrapper_812f9ce7e5aadc6b316f29b4b58f7fcc.RData b/blogdown/en/sp/spr/steps_cache/html/edger_wrapper_812f9ce7e5aadc6b316f29b4b58f7fcc.RData new file mode 100644 index 000000000..c0c17aa48 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/edger_wrapper_812f9ce7e5aadc6b316f29b4b58f7fcc.RData differ diff --git a/content/en/sp/spr/steps_cache/html/edger_wrapper_1c7ea98bdb048701e6b14cf866decf9a.rdb b/blogdown/en/sp/spr/steps_cache/html/edger_wrapper_812f9ce7e5aadc6b316f29b4b58f7fcc.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/edger_wrapper_1c7ea98bdb048701e6b14cf866decf9a.rdb rename to blogdown/en/sp/spr/steps_cache/html/edger_wrapper_812f9ce7e5aadc6b316f29b4b58f7fcc.rdb diff --git a/content/en/sp/spr/steps_cache/html/edger_wrapper_1c7ea98bdb048701e6b14cf866decf9a.rdx b/blogdown/en/sp/spr/steps_cache/html/edger_wrapper_812f9ce7e5aadc6b316f29b4b58f7fcc.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/edger_wrapper_1c7ea98bdb048701e6b14cf866decf9a.rdx rename to blogdown/en/sp/spr/steps_cache/html/edger_wrapper_812f9ce7e5aadc6b316f29b4b58f7fcc.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/fastq_quality_a043cbf691f8c697b612554b66dfbd1f.RData b/blogdown/en/sp/spr/steps_cache/html/fastq_quality_a043cbf691f8c697b612554b66dfbd1f.RData new file mode 100644 index 000000000..2f89d5fa4 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/fastq_quality_a043cbf691f8c697b612554b66dfbd1f.RData differ diff --git a/content/en/sp/spr/steps_cache/html/sample_tree_rpkm_1f9226dec5d65932acf8cdc1853468ea.rdb b/blogdown/en/sp/spr/steps_cache/html/fastq_quality_a043cbf691f8c697b612554b66dfbd1f.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/sample_tree_rpkm_1f9226dec5d65932acf8cdc1853468ea.rdb rename to blogdown/en/sp/spr/steps_cache/html/fastq_quality_a043cbf691f8c697b612554b66dfbd1f.rdb diff --git a/content/en/sp/spr/steps_cache/html/sample_tree_rpkm_1f9226dec5d65932acf8cdc1853468ea.rdx b/blogdown/en/sp/spr/steps_cache/html/fastq_quality_a043cbf691f8c697b612554b66dfbd1f.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/sample_tree_rpkm_1f9226dec5d65932acf8cdc1853468ea.rdx rename to blogdown/en/sp/spr/steps_cache/html/fastq_quality_a043cbf691f8c697b612554b66dfbd1f.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/fastq_quality_parallel_cluster_5930e862fa2c06bba1ddefa75a6b12a2.RData b/blogdown/en/sp/spr/steps_cache/html/fastq_quality_parallel_cluster_5930e862fa2c06bba1ddefa75a6b12a2.RData new file mode 100644 index 000000000..2498138f5 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/fastq_quality_parallel_cluster_5930e862fa2c06bba1ddefa75a6b12a2.RData differ diff --git a/content/en/sp/spr/steps_cache/html/setup_2fda07be3e05c55236ab5847520a2087.rdb b/blogdown/en/sp/spr/steps_cache/html/fastq_quality_parallel_cluster_5930e862fa2c06bba1ddefa75a6b12a2.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/setup_2fda07be3e05c55236ab5847520a2087.rdb rename to blogdown/en/sp/spr/steps_cache/html/fastq_quality_parallel_cluster_5930e862fa2c06bba1ddefa75a6b12a2.rdb diff --git a/content/en/sp/spr/steps_cache/html/setup_2fda07be3e05c55236ab5847520a2087.rdx b/blogdown/en/sp/spr/steps_cache/html/fastq_quality_parallel_cluster_5930e862fa2c06bba1ddefa75a6b12a2.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/setup_2fda07be3e05c55236ab5847520a2087.rdx rename to blogdown/en/sp/spr/steps_cache/html/fastq_quality_parallel_cluster_5930e862fa2c06bba1ddefa75a6b12a2.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/fastq_quality_parallel_single_c1c22d513aeb52b380886b80d7cf724b.RData b/blogdown/en/sp/spr/steps_cache/html/fastq_quality_parallel_single_c1c22d513aeb52b380886b80d7cf724b.RData new file mode 100644 index 000000000..5f71150eb Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/fastq_quality_parallel_single_c1c22d513aeb52b380886b80d7cf724b.RData differ diff --git a/content/en/sp/spr/steps_cache/html/subset_22f1033586d00a8365e3c1c4a555d7f2.rdb b/blogdown/en/sp/spr/steps_cache/html/fastq_quality_parallel_single_c1c22d513aeb52b380886b80d7cf724b.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/subset_22f1033586d00a8365e3c1c4a555d7f2.rdb rename to blogdown/en/sp/spr/steps_cache/html/fastq_quality_parallel_single_c1c22d513aeb52b380886b80d7cf724b.rdb diff --git a/content/en/sp/spr/steps_cache/html/subset_22f1033586d00a8365e3c1c4a555d7f2.rdx b/blogdown/en/sp/spr/steps_cache/html/fastq_quality_parallel_single_c1c22d513aeb52b380886b80d7cf724b.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/subset_22f1033586d00a8365e3c1c4a555d7f2.rdx rename to blogdown/en/sp/spr/steps_cache/html/fastq_quality_parallel_single_c1c22d513aeb52b380886b80d7cf724b.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/get_go_biomart_3168324c96b7503b8bea4e31e403b9f3.RData b/blogdown/en/sp/spr/steps_cache/html/get_go_biomart_3168324c96b7503b8bea4e31e403b9f3.RData new file mode 100644 index 000000000..113ac666f Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/get_go_biomart_3168324c96b7503b8bea4e31e403b9f3.RData differ diff --git a/content/en/sp/spr/steps_cache/html/tophat2-pe_39e3d4ebb1c6758ad27f70af59ec263b.rdb b/blogdown/en/sp/spr/steps_cache/html/get_go_biomart_3168324c96b7503b8bea4e31e403b9f3.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/tophat2-pe_39e3d4ebb1c6758ad27f70af59ec263b.rdb rename to blogdown/en/sp/spr/steps_cache/html/get_go_biomart_3168324c96b7503b8bea4e31e403b9f3.rdb diff --git a/content/en/sp/spr/steps_cache/html/tophat2-pe_39e3d4ebb1c6758ad27f70af59ec263b.rdx b/blogdown/en/sp/spr/steps_cache/html/get_go_biomart_3168324c96b7503b8bea4e31e403b9f3.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/tophat2-pe_39e3d4ebb1c6758ad27f70af59ec263b.rdx rename to blogdown/en/sp/spr/steps_cache/html/get_go_biomart_3168324c96b7503b8bea4e31e403b9f3.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/go_enrichment_a398c83f7d02024aab9e5e150ff5e13e.RData b/blogdown/en/sp/spr/steps_cache/html/go_enrichment_a398c83f7d02024aab9e5e150ff5e13e.RData new file mode 100644 index 000000000..237792819 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/go_enrichment_a398c83f7d02024aab9e5e150ff5e13e.RData differ diff --git a/content/en/sp/spr/steps_cache/html/tophat2-pe_parallel_0258d3c3463d17bf2fd452604716766c.rdb b/blogdown/en/sp/spr/steps_cache/html/go_enrichment_a398c83f7d02024aab9e5e150ff5e13e.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/tophat2-pe_parallel_0258d3c3463d17bf2fd452604716766c.rdb rename to blogdown/en/sp/spr/steps_cache/html/go_enrichment_a398c83f7d02024aab9e5e150ff5e13e.rdb diff --git a/content/en/sp/spr/steps_cache/html/tophat2-pe_parallel_0258d3c3463d17bf2fd452604716766c.rdx b/blogdown/en/sp/spr/steps_cache/html/go_enrichment_a398c83f7d02024aab9e5e150ff5e13e.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/tophat2-pe_parallel_0258d3c3463d17bf2fd452604716766c.rdx rename to blogdown/en/sp/spr/steps_cache/html/go_enrichment_a398c83f7d02024aab9e5e150ff5e13e.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/gsnap_86c745883aaf259c887eda976f529203.RData b/blogdown/en/sp/spr/steps_cache/html/gsnap_86c745883aaf259c887eda976f529203.RData new file mode 100644 index 000000000..c31f542e1 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/gsnap_86c745883aaf259c887eda976f529203.RData differ diff --git a/content/en/sp/spr/steps_cache/html/trimGalore_1d27f0b61e1f1a75ea8a5e860695f1e5.rdb b/blogdown/en/sp/spr/steps_cache/html/gsnap_86c745883aaf259c887eda976f529203.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/trimGalore_1d27f0b61e1f1a75ea8a5e860695f1e5.rdb rename to blogdown/en/sp/spr/steps_cache/html/gsnap_86c745883aaf259c887eda976f529203.rdb diff --git a/content/en/sp/spr/steps_cache/html/trimGalore_1d27f0b61e1f1a75ea8a5e860695f1e5.rdx b/blogdown/en/sp/spr/steps_cache/html/gsnap_86c745883aaf259c887eda976f529203.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/trimGalore_1d27f0b61e1f1a75ea8a5e860695f1e5.rdx rename to blogdown/en/sp/spr/steps_cache/html/gsnap_86c745883aaf259c887eda976f529203.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/hierarchical_clustering_bf9334202a8f2aa138adbfd8ba8b9004.RData b/blogdown/en/sp/spr/steps_cache/html/hierarchical_clustering_bf9334202a8f2aa138adbfd8ba8b9004.RData new file mode 100644 index 000000000..5a9b01017 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/hierarchical_clustering_bf9334202a8f2aa138adbfd8ba8b9004.RData differ diff --git a/content/en/sp/spr/steps_cache/html/trimmomatic_c1337f35f54014372a282bd4f7c28658.rdb b/blogdown/en/sp/spr/steps_cache/html/hierarchical_clustering_bf9334202a8f2aa138adbfd8ba8b9004.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/trimmomatic_c1337f35f54014372a282bd4f7c28658.rdb rename to blogdown/en/sp/spr/steps_cache/html/hierarchical_clustering_bf9334202a8f2aa138adbfd8ba8b9004.rdb diff --git a/content/en/sp/spr/steps_cache/html/trimmomatic_c1337f35f54014372a282bd4f7c28658.rdx b/blogdown/en/sp/spr/steps_cache/html/hierarchical_clustering_bf9334202a8f2aa138adbfd8ba8b9004.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/trimmomatic_c1337f35f54014372a282bd4f7c28658.rdx rename to blogdown/en/sp/spr/steps_cache/html/hierarchical_clustering_bf9334202a8f2aa138adbfd8ba8b9004.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/hisat_SYSargs2_object_cee2d481d5bc62cd9bd9552681ca40ac.RData b/blogdown/en/sp/spr/steps_cache/html/hisat_SYSargs2_object_cee2d481d5bc62cd9bd9552681ca40ac.RData new file mode 100644 index 000000000..d949e912d Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/hisat_SYSargs2_object_cee2d481d5bc62cd9bd9552681ca40ac.RData differ diff --git a/blogdown/en/sp/spr/steps_cache/html/hisat_SYSargs2_object_cee2d481d5bc62cd9bd9552681ca40ac.rdb b/blogdown/en/sp/spr/steps_cache/html/hisat_SYSargs2_object_cee2d481d5bc62cd9bd9552681ca40ac.rdb new file mode 100644 index 000000000..cbda37563 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/hisat_SYSargs2_object_cee2d481d5bc62cd9bd9552681ca40ac.rdb differ diff --git a/blogdown/en/sp/spr/steps_cache/html/hisat_SYSargs2_object_cee2d481d5bc62cd9bd9552681ca40ac.rdx b/blogdown/en/sp/spr/steps_cache/html/hisat_SYSargs2_object_cee2d481d5bc62cd9bd9552681ca40ac.rdx new file mode 100644 index 000000000..97cc83779 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/hisat_SYSargs2_object_cee2d481d5bc62cd9bd9552681ca40ac.rdx differ diff --git a/blogdown/en/sp/spr/steps_cache/html/hisat_alignment_77a56be64debcd838768ff7ba4a88b45.RData b/blogdown/en/sp/spr/steps_cache/html/hisat_alignment_77a56be64debcd838768ff7ba4a88b45.RData new file mode 100644 index 000000000..de6151561 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/hisat_alignment_77a56be64debcd838768ff7ba4a88b45.RData differ diff --git a/content/en/sp/spr/steps_cache/html/writeTargetsout_bbc83c7921f23b96205e3f06cdebb350.rdb b/blogdown/en/sp/spr/steps_cache/html/hisat_alignment_77a56be64debcd838768ff7ba4a88b45.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/writeTargetsout_bbc83c7921f23b96205e3f06cdebb350.rdb rename to blogdown/en/sp/spr/steps_cache/html/hisat_alignment_77a56be64debcd838768ff7ba4a88b45.rdb diff --git a/content/en/sp/spr/steps_cache/html/writeTargetsout_bbc83c7921f23b96205e3f06cdebb350.rdx b/blogdown/en/sp/spr/steps_cache/html/hisat_alignment_77a56be64debcd838768ff7ba4a88b45.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/writeTargetsout_bbc83c7921f23b96205e3f06cdebb350.rdx rename to blogdown/en/sp/spr/steps_cache/html/hisat_alignment_77a56be64debcd838768ff7ba4a88b45.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/hisat_index_3a047704386bd2711c04185f63af28a8.RData b/blogdown/en/sp/spr/steps_cache/html/hisat_index_3a047704386bd2711c04185f63af28a8.RData new file mode 100644 index 000000000..1763abba0 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/hisat_index_3a047704386bd2711c04185f63af28a8.RData differ diff --git a/content/en/sp/spr/steps_cache/html/writeTargetsout_bowtiePE_c490e07d97c5e44329f43281434c7c70.rdb b/blogdown/en/sp/spr/steps_cache/html/hisat_index_3a047704386bd2711c04185f63af28a8.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/writeTargetsout_bowtiePE_c490e07d97c5e44329f43281434c7c70.rdb rename to blogdown/en/sp/spr/steps_cache/html/hisat_index_3a047704386bd2711c04185f63af28a8.rdb diff --git a/content/en/sp/spr/steps_cache/html/writeTargetsout_bowtiePE_c490e07d97c5e44329f43281434c7c70.rdx b/blogdown/en/sp/spr/steps_cache/html/hisat_index_3a047704386bd2711c04185f63af28a8.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/writeTargetsout_bowtiePE_c490e07d97c5e44329f43281434c7c70.rdx rename to blogdown/en/sp/spr/steps_cache/html/hisat_index_3a047704386bd2711c04185f63af28a8.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/igv_fc1e7f5854c379df53bff2dbfa04c07e.RData b/blogdown/en/sp/spr/steps_cache/html/igv_fc1e7f5854c379df53bff2dbfa04c07e.RData new file mode 100644 index 000000000..54c21f8c4 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/igv_fc1e7f5854c379df53bff2dbfa04c07e.RData differ diff --git a/content/en/sp/spr/steps_cache/html/writeTargetsout_bwaPE_73573f9488148085e18501ae1cd1b04c.rdb b/blogdown/en/sp/spr/steps_cache/html/igv_fc1e7f5854c379df53bff2dbfa04c07e.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/writeTargetsout_bwaPE_73573f9488148085e18501ae1cd1b04c.rdb rename to blogdown/en/sp/spr/steps_cache/html/igv_fc1e7f5854c379df53bff2dbfa04c07e.rdb diff --git a/content/en/sp/spr/steps_cache/html/writeTargetsout_bwaPE_73573f9488148085e18501ae1cd1b04c.rdx b/blogdown/en/sp/spr/steps_cache/html/igv_fc1e7f5854c379df53bff2dbfa04c07e.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/writeTargetsout_bwaPE_73573f9488148085e18501ae1cd1b04c.rdx rename to blogdown/en/sp/spr/steps_cache/html/igv_fc1e7f5854c379df53bff2dbfa04c07e.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/load_package_687920534f55eca0c3c599a08f4fe7b1.RData b/blogdown/en/sp/spr/steps_cache/html/load_package_687920534f55eca0c3c599a08f4fe7b1.RData new file mode 100644 index 000000000..b11e694a8 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/load_package_687920534f55eca0c3c599a08f4fe7b1.RData differ diff --git a/content/en/sp/spr/steps_cache/html/writeTargetsout_gsnap_b7bd00114f269283ee7a9b41aa32cd3f.rdb b/blogdown/en/sp/spr/steps_cache/html/load_package_687920534f55eca0c3c599a08f4fe7b1.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/writeTargetsout_gsnap_b7bd00114f269283ee7a9b41aa32cd3f.rdb rename to blogdown/en/sp/spr/steps_cache/html/load_package_687920534f55eca0c3c599a08f4fe7b1.rdb diff --git a/content/en/sp/spr/steps_cache/html/writeTargetsout_gsnap_b7bd00114f269283ee7a9b41aa32cd3f.rdx b/blogdown/en/sp/spr/steps_cache/html/load_package_687920534f55eca0c3c599a08f4fe7b1.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/writeTargetsout_gsnap_b7bd00114f269283ee7a9b41aa32cd3f.rdx rename to blogdown/en/sp/spr/steps_cache/html/load_package_687920534f55eca0c3c599a08f4fe7b1.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/output_45955bf2307d4138648c30adc53afa5f.RData b/blogdown/en/sp/spr/steps_cache/html/output_45955bf2307d4138648c30adc53afa5f.RData new file mode 100644 index 000000000..4d73d44cd Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/output_45955bf2307d4138648c30adc53afa5f.RData differ diff --git a/content/en/sp/spr/steps_cache/html/writeTargetsout_rsubread_5b07227a78e433d4d8e5894b06d1a5c3.rdb b/blogdown/en/sp/spr/steps_cache/html/output_45955bf2307d4138648c30adc53afa5f.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/writeTargetsout_rsubread_5b07227a78e433d4d8e5894b06d1a5c3.rdb rename to blogdown/en/sp/spr/steps_cache/html/output_45955bf2307d4138648c30adc53afa5f.rdb diff --git a/content/en/sp/spr/steps_cache/html/writeTargetsout_rsubread_5b07227a78e433d4d8e5894b06d1a5c3.rdx b/blogdown/en/sp/spr/steps_cache/html/output_45955bf2307d4138648c30adc53afa5f.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/writeTargetsout_rsubread_5b07227a78e433d4d8e5894b06d1a5c3.rdx rename to blogdown/en/sp/spr/steps_cache/html/output_45955bf2307d4138648c30adc53afa5f.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/plot_go_enrichment_57b055cbc105081b847cf8e95cda6642.RData b/blogdown/en/sp/spr/steps_cache/html/plot_go_enrichment_57b055cbc105081b847cf8e95cda6642.RData new file mode 100644 index 000000000..b86648689 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/plot_go_enrichment_57b055cbc105081b847cf8e95cda6642.RData differ diff --git a/content/en/sp/spr/steps_cache/html/writeTargetsout_tophat2PE_0f67b9ef6f60e38e525300baa3ff35af.rdb b/blogdown/en/sp/spr/steps_cache/html/plot_go_enrichment_57b055cbc105081b847cf8e95cda6642.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/writeTargetsout_tophat2PE_0f67b9ef6f60e38e525300baa3ff35af.rdb rename to blogdown/en/sp/spr/steps_cache/html/plot_go_enrichment_57b055cbc105081b847cf8e95cda6642.rdb diff --git a/content/en/sp/spr/steps_cache/html/writeTargetsout_tophat2PE_0f67b9ef6f60e38e525300baa3ff35af.rdx b/blogdown/en/sp/spr/steps_cache/html/plot_go_enrichment_57b055cbc105081b847cf8e95cda6642.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/writeTargetsout_tophat2PE_0f67b9ef6f60e38e525300baa3ff35af.rdx rename to blogdown/en/sp/spr/steps_cache/html/plot_go_enrichment_57b055cbc105081b847cf8e95cda6642.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/preprocessing_a244441f267cbda2f639670931750f8e.RData b/blogdown/en/sp/spr/steps_cache/html/preprocessing_a244441f267cbda2f639670931750f8e.RData new file mode 100644 index 000000000..c5d7c859e Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/preprocessing_a244441f267cbda2f639670931750f8e.RData differ diff --git a/blogdown/en/sp/spr/steps_cache/html/preprocessing_a244441f267cbda2f639670931750f8e.rdb b/blogdown/en/sp/spr/steps_cache/html/preprocessing_a244441f267cbda2f639670931750f8e.rdb new file mode 100644 index 000000000..e69de29bb diff --git a/blogdown/en/sp/spr/steps_cache/html/preprocessing_a244441f267cbda2f639670931750f8e.rdx b/blogdown/en/sp/spr/steps_cache/html/preprocessing_a244441f267cbda2f639670931750f8e.rdx new file mode 100644 index 000000000..99a1b29ad Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/preprocessing_a244441f267cbda2f639670931750f8e.rdx differ diff --git a/blogdown/en/sp/spr/steps_cache/html/process_monitoring_984453409c373bd97bd05499b020ae29.RData b/blogdown/en/sp/spr/steps_cache/html/process_monitoring_984453409c373bd97bd05499b020ae29.RData new file mode 100644 index 000000000..5e8274546 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/process_monitoring_984453409c373bd97bd05499b020ae29.RData differ diff --git a/blogdown/en/sp/spr/steps_cache/html/process_monitoring_984453409c373bd97bd05499b020ae29.rdb b/blogdown/en/sp/spr/steps_cache/html/process_monitoring_984453409c373bd97bd05499b020ae29.rdb new file mode 100644 index 000000000..e69de29bb diff --git a/blogdown/en/sp/spr/steps_cache/html/process_monitoring_984453409c373bd97bd05499b020ae29.rdx b/blogdown/en/sp/spr/steps_cache/html/process_monitoring_984453409c373bd97bd05499b020ae29.rdx new file mode 100644 index 000000000..99a1b29ad Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/process_monitoring_984453409c373bd97bd05499b020ae29.rdx differ diff --git a/blogdown/en/sp/spr/steps_cache/html/read_counting_mirna_df23bbcf4d853dd569b5aa11c305c785.RData b/blogdown/en/sp/spr/steps_cache/html/read_counting_mirna_df23bbcf4d853dd569b5aa11c305c785.RData new file mode 100644 index 000000000..32e46af4b Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/read_counting_mirna_df23bbcf4d853dd569b5aa11c305c785.RData differ diff --git a/blogdown/en/sp/spr/steps_cache/html/read_counting_mirna_df23bbcf4d853dd569b5aa11c305c785.rdb b/blogdown/en/sp/spr/steps_cache/html/read_counting_mirna_df23bbcf4d853dd569b5aa11c305c785.rdb new file mode 100644 index 000000000..e69de29bb diff --git a/blogdown/en/sp/spr/steps_cache/html/read_counting_mirna_df23bbcf4d853dd569b5aa11c305c785.rdx b/blogdown/en/sp/spr/steps_cache/html/read_counting_mirna_df23bbcf4d853dd569b5aa11c305c785.rdx new file mode 100644 index 000000000..99a1b29ad Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/read_counting_mirna_df23bbcf4d853dd569b5aa11c305c785.rdx differ diff --git a/blogdown/en/sp/spr/steps_cache/html/read_counting_multicore_5305ed412adf89d921e0e024b5cdaf6d.RData b/blogdown/en/sp/spr/steps_cache/html/read_counting_multicore_5305ed412adf89d921e0e024b5cdaf6d.RData new file mode 100644 index 000000000..39a24be3f Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/read_counting_multicore_5305ed412adf89d921e0e024b5cdaf6d.RData differ diff --git a/blogdown/en/sp/spr/steps_cache/html/read_counting_multicore_5305ed412adf89d921e0e024b5cdaf6d.rdb b/blogdown/en/sp/spr/steps_cache/html/read_counting_multicore_5305ed412adf89d921e0e024b5cdaf6d.rdb new file mode 100644 index 000000000..e69de29bb diff --git a/blogdown/en/sp/spr/steps_cache/html/read_counting_multicore_5305ed412adf89d921e0e024b5cdaf6d.rdx b/blogdown/en/sp/spr/steps_cache/html/read_counting_multicore_5305ed412adf89d921e0e024b5cdaf6d.rdx new file mode 100644 index 000000000..99a1b29ad Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/read_counting_multicore_5305ed412adf89d921e0e024b5cdaf6d.rdx differ diff --git a/blogdown/en/sp/spr/steps_cache/html/read_counting_multinode_74cf29033a84963d0ab065feb34ab75a.RData b/blogdown/en/sp/spr/steps_cache/html/read_counting_multinode_74cf29033a84963d0ab065feb34ab75a.RData new file mode 100644 index 000000000..adf98699f Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/read_counting_multinode_74cf29033a84963d0ab065feb34ab75a.RData differ diff --git a/blogdown/en/sp/spr/steps_cache/html/read_counting_multinode_74cf29033a84963d0ab065feb34ab75a.rdb b/blogdown/en/sp/spr/steps_cache/html/read_counting_multinode_74cf29033a84963d0ab065feb34ab75a.rdb new file mode 100644 index 000000000..e69de29bb diff --git a/blogdown/en/sp/spr/steps_cache/html/read_counting_multinode_74cf29033a84963d0ab065feb34ab75a.rdx b/blogdown/en/sp/spr/steps_cache/html/read_counting_multinode_74cf29033a84963d0ab065feb34ab75a.rdx new file mode 100644 index 000000000..99a1b29ad Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/read_counting_multinode_74cf29033a84963d0ab065feb34ab75a.rdx differ diff --git a/blogdown/en/sp/spr/steps_cache/html/rsubread_5f8fb3a103bb5fd8420786ed2e5d5d67.RData b/blogdown/en/sp/spr/steps_cache/html/rsubread_5f8fb3a103bb5fd8420786ed2e5d5d67.RData new file mode 100644 index 000000000..b697daf8f Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/rsubread_5f8fb3a103bb5fd8420786ed2e5d5d67.RData differ diff --git a/blogdown/en/sp/spr/steps_cache/html/rsubread_5f8fb3a103bb5fd8420786ed2e5d5d67.rdb b/blogdown/en/sp/spr/steps_cache/html/rsubread_5f8fb3a103bb5fd8420786ed2e5d5d67.rdb new file mode 100644 index 000000000..e69de29bb diff --git a/blogdown/en/sp/spr/steps_cache/html/rsubread_5f8fb3a103bb5fd8420786ed2e5d5d67.rdx b/blogdown/en/sp/spr/steps_cache/html/rsubread_5f8fb3a103bb5fd8420786ed2e5d5d67.rdx new file mode 100644 index 000000000..99a1b29ad Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/rsubread_5f8fb3a103bb5fd8420786ed2e5d5d67.rdx differ diff --git a/blogdown/en/sp/spr/steps_cache/html/runCommandline_align_ab0102d9aaa91dfc24b8aae41657ddaa.RData b/blogdown/en/sp/spr/steps_cache/html/runCommandline_align_ab0102d9aaa91dfc24b8aae41657ddaa.RData new file mode 100644 index 000000000..053eca3e0 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/runCommandline_align_ab0102d9aaa91dfc24b8aae41657ddaa.RData differ diff --git a/blogdown/en/sp/spr/steps_cache/html/runCommandline_align_ab0102d9aaa91dfc24b8aae41657ddaa.rdb b/blogdown/en/sp/spr/steps_cache/html/runCommandline_align_ab0102d9aaa91dfc24b8aae41657ddaa.rdb new file mode 100644 index 000000000..e69de29bb diff --git a/blogdown/en/sp/spr/steps_cache/html/runCommandline_align_ab0102d9aaa91dfc24b8aae41657ddaa.rdx b/blogdown/en/sp/spr/steps_cache/html/runCommandline_align_ab0102d9aaa91dfc24b8aae41657ddaa.rdx new file mode 100644 index 000000000..99a1b29ad Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/runCommandline_align_ab0102d9aaa91dfc24b8aae41657ddaa.rdx differ diff --git a/blogdown/en/sp/spr/steps_cache/html/sample_tree_rlog_dfba617e2275bab16dab41ac6518c1aa.RData b/blogdown/en/sp/spr/steps_cache/html/sample_tree_rlog_dfba617e2275bab16dab41ac6518c1aa.RData new file mode 100644 index 000000000..c1e9bab8e Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/sample_tree_rlog_dfba617e2275bab16dab41ac6518c1aa.RData differ diff --git a/content/en/sp/spr/steps_cache/html/sample_tree_rlog_c81b1c899f1daced817d4fd4c5db16a5.rdb b/blogdown/en/sp/spr/steps_cache/html/sample_tree_rlog_dfba617e2275bab16dab41ac6518c1aa.rdb similarity index 98% rename from content/en/sp/spr/steps_cache/html/sample_tree_rlog_c81b1c899f1daced817d4fd4c5db16a5.rdb rename to blogdown/en/sp/spr/steps_cache/html/sample_tree_rlog_dfba617e2275bab16dab41ac6518c1aa.rdb index ab375f15a..33ca08f9f 100644 Binary files a/content/en/sp/spr/steps_cache/html/sample_tree_rlog_c81b1c899f1daced817d4fd4c5db16a5.rdb and b/blogdown/en/sp/spr/steps_cache/html/sample_tree_rlog_dfba617e2275bab16dab41ac6518c1aa.rdb differ diff --git a/content/en/sp/spr/steps_cache/html/sample_tree_rlog_c81b1c899f1daced817d4fd4c5db16a5.rdx b/blogdown/en/sp/spr/steps_cache/html/sample_tree_rlog_dfba617e2275bab16dab41ac6518c1aa.rdx similarity index 60% rename from content/en/sp/spr/steps_cache/html/sample_tree_rlog_c81b1c899f1daced817d4fd4c5db16a5.rdx rename to blogdown/en/sp/spr/steps_cache/html/sample_tree_rlog_dfba617e2275bab16dab41ac6518c1aa.rdx index 0ac38425c..3d629a277 100644 Binary files a/content/en/sp/spr/steps_cache/html/sample_tree_rlog_c81b1c899f1daced817d4fd4c5db16a5.rdx and b/blogdown/en/sp/spr/steps_cache/html/sample_tree_rlog_dfba617e2275bab16dab41ac6518c1aa.rdx differ diff --git a/blogdown/en/sp/spr/steps_cache/html/sample_tree_rpkm_e6d1049e27de516ab69248d47308a78a.RData b/blogdown/en/sp/spr/steps_cache/html/sample_tree_rpkm_e6d1049e27de516ab69248d47308a78a.RData new file mode 100644 index 000000000..d9adddc23 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/sample_tree_rpkm_e6d1049e27de516ab69248d47308a78a.RData differ diff --git a/blogdown/en/sp/spr/steps_cache/html/sample_tree_rpkm_e6d1049e27de516ab69248d47308a78a.rdb b/blogdown/en/sp/spr/steps_cache/html/sample_tree_rpkm_e6d1049e27de516ab69248d47308a78a.rdb new file mode 100644 index 000000000..e69de29bb diff --git a/blogdown/en/sp/spr/steps_cache/html/sample_tree_rpkm_e6d1049e27de516ab69248d47308a78a.rdx b/blogdown/en/sp/spr/steps_cache/html/sample_tree_rpkm_e6d1049e27de516ab69248d47308a78a.rdx new file mode 100644 index 000000000..99a1b29ad Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/sample_tree_rpkm_e6d1049e27de516ab69248d47308a78a.rdx differ diff --git a/blogdown/en/sp/spr/steps_cache/html/setup_3cbfd5b0a3fc3a205925a05c22c50dbc.RData b/blogdown/en/sp/spr/steps_cache/html/setup_3cbfd5b0a3fc3a205925a05c22c50dbc.RData new file mode 100644 index 000000000..db39ff7ef Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/setup_3cbfd5b0a3fc3a205925a05c22c50dbc.RData differ diff --git a/blogdown/en/sp/spr/steps_cache/html/setup_3cbfd5b0a3fc3a205925a05c22c50dbc.rdb b/blogdown/en/sp/spr/steps_cache/html/setup_3cbfd5b0a3fc3a205925a05c22c50dbc.rdb new file mode 100644 index 000000000..e69de29bb diff --git a/blogdown/en/sp/spr/steps_cache/html/setup_3cbfd5b0a3fc3a205925a05c22c50dbc.rdx b/blogdown/en/sp/spr/steps_cache/html/setup_3cbfd5b0a3fc3a205925a05c22c50dbc.rdx new file mode 100644 index 000000000..99a1b29ad Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/setup_3cbfd5b0a3fc3a205925a05c22c50dbc.rdx differ diff --git a/blogdown/en/sp/spr/steps_cache/html/subset_a3a54e728976ccff12a950e6567d0cb8.RData b/blogdown/en/sp/spr/steps_cache/html/subset_a3a54e728976ccff12a950e6567d0cb8.RData new file mode 100644 index 000000000..bf921d004 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/subset_a3a54e728976ccff12a950e6567d0cb8.RData differ diff --git a/blogdown/en/sp/spr/steps_cache/html/subset_a3a54e728976ccff12a950e6567d0cb8.rdb b/blogdown/en/sp/spr/steps_cache/html/subset_a3a54e728976ccff12a950e6567d0cb8.rdb new file mode 100644 index 000000000..e69de29bb diff --git a/blogdown/en/sp/spr/steps_cache/html/subset_a3a54e728976ccff12a950e6567d0cb8.rdx b/blogdown/en/sp/spr/steps_cache/html/subset_a3a54e728976ccff12a950e6567d0cb8.rdx new file mode 100644 index 000000000..99a1b29ad Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/subset_a3a54e728976ccff12a950e6567d0cb8.rdx differ diff --git a/blogdown/en/sp/spr/steps_cache/html/tophat2-pe_f498b685a7ba0e87e765b010ad0d596d.RData b/blogdown/en/sp/spr/steps_cache/html/tophat2-pe_f498b685a7ba0e87e765b010ad0d596d.RData new file mode 100644 index 000000000..75dc78a05 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/tophat2-pe_f498b685a7ba0e87e765b010ad0d596d.RData differ diff --git a/blogdown/en/sp/spr/steps_cache/html/tophat2-pe_f498b685a7ba0e87e765b010ad0d596d.rdb b/blogdown/en/sp/spr/steps_cache/html/tophat2-pe_f498b685a7ba0e87e765b010ad0d596d.rdb new file mode 100644 index 000000000..e69de29bb diff --git a/blogdown/en/sp/spr/steps_cache/html/tophat2-pe_f498b685a7ba0e87e765b010ad0d596d.rdx b/blogdown/en/sp/spr/steps_cache/html/tophat2-pe_f498b685a7ba0e87e765b010ad0d596d.rdx new file mode 100644 index 000000000..99a1b29ad Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/tophat2-pe_f498b685a7ba0e87e765b010ad0d596d.rdx differ diff --git a/blogdown/en/sp/spr/steps_cache/html/tophat2-pe_parallel_8fd781ff645c1208ee4ddb02ff6474ef.RData b/blogdown/en/sp/spr/steps_cache/html/tophat2-pe_parallel_8fd781ff645c1208ee4ddb02ff6474ef.RData new file mode 100644 index 000000000..ae3d39a24 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/tophat2-pe_parallel_8fd781ff645c1208ee4ddb02ff6474ef.RData differ diff --git a/blogdown/en/sp/spr/steps_cache/html/tophat2-pe_parallel_8fd781ff645c1208ee4ddb02ff6474ef.rdb b/blogdown/en/sp/spr/steps_cache/html/tophat2-pe_parallel_8fd781ff645c1208ee4ddb02ff6474ef.rdb new file mode 100644 index 000000000..e69de29bb diff --git a/blogdown/en/sp/spr/steps_cache/html/tophat2-pe_parallel_8fd781ff645c1208ee4ddb02ff6474ef.rdx b/blogdown/en/sp/spr/steps_cache/html/tophat2-pe_parallel_8fd781ff645c1208ee4ddb02ff6474ef.rdx new file mode 100644 index 000000000..99a1b29ad Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/tophat2-pe_parallel_8fd781ff645c1208ee4ddb02ff6474ef.rdx differ diff --git a/blogdown/en/sp/spr/steps_cache/html/trimGalore_b1cfb8e6363f99c230e98894beb63c5b.RData b/blogdown/en/sp/spr/steps_cache/html/trimGalore_b1cfb8e6363f99c230e98894beb63c5b.RData new file mode 100644 index 000000000..c669b3b90 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/trimGalore_b1cfb8e6363f99c230e98894beb63c5b.RData differ diff --git a/blogdown/en/sp/spr/steps_cache/html/trimGalore_b1cfb8e6363f99c230e98894beb63c5b.rdb b/blogdown/en/sp/spr/steps_cache/html/trimGalore_b1cfb8e6363f99c230e98894beb63c5b.rdb new file mode 100644 index 000000000..e69de29bb diff --git a/blogdown/en/sp/spr/steps_cache/html/trimGalore_b1cfb8e6363f99c230e98894beb63c5b.rdx b/blogdown/en/sp/spr/steps_cache/html/trimGalore_b1cfb8e6363f99c230e98894beb63c5b.rdx new file mode 100644 index 000000000..99a1b29ad Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/trimGalore_b1cfb8e6363f99c230e98894beb63c5b.rdx differ diff --git a/blogdown/en/sp/spr/steps_cache/html/trimmomatic_e32e9b73a212ed3a853f4bea921f18d4.RData b/blogdown/en/sp/spr/steps_cache/html/trimmomatic_e32e9b73a212ed3a853f4bea921f18d4.RData new file mode 100644 index 000000000..1276b4efc Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/trimmomatic_e32e9b73a212ed3a853f4bea921f18d4.RData differ diff --git a/blogdown/en/sp/spr/steps_cache/html/trimmomatic_e32e9b73a212ed3a853f4bea921f18d4.rdb b/blogdown/en/sp/spr/steps_cache/html/trimmomatic_e32e9b73a212ed3a853f4bea921f18d4.rdb new file mode 100644 index 000000000..e69de29bb diff --git a/blogdown/en/sp/spr/steps_cache/html/trimmomatic_e32e9b73a212ed3a853f4bea921f18d4.rdx b/blogdown/en/sp/spr/steps_cache/html/trimmomatic_e32e9b73a212ed3a853f4bea921f18d4.rdx new file mode 100644 index 000000000..99a1b29ad Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/trimmomatic_e32e9b73a212ed3a853f4bea921f18d4.rdx differ diff --git a/blogdown/en/sp/spr/steps_cache/html/vennplot_cd8ec7b8c4dd60491e94fd04608b7e9d.RData b/blogdown/en/sp/spr/steps_cache/html/vennplot_cd8ec7b8c4dd60491e94fd04608b7e9d.RData new file mode 100644 index 000000000..f54bad162 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/vennplot_cd8ec7b8c4dd60491e94fd04608b7e9d.RData differ diff --git a/content/en/sp/spr/steps_cache/html/vennplot_4adb227323bb9b1404fce13c3a059901.rdb b/blogdown/en/sp/spr/steps_cache/html/vennplot_cd8ec7b8c4dd60491e94fd04608b7e9d.rdb similarity index 100% rename from content/en/sp/spr/steps_cache/html/vennplot_4adb227323bb9b1404fce13c3a059901.rdb rename to blogdown/en/sp/spr/steps_cache/html/vennplot_cd8ec7b8c4dd60491e94fd04608b7e9d.rdb diff --git a/content/en/sp/spr/steps_cache/html/vennplot_4adb227323bb9b1404fce13c3a059901.rdx b/blogdown/en/sp/spr/steps_cache/html/vennplot_cd8ec7b8c4dd60491e94fd04608b7e9d.rdx similarity index 100% rename from content/en/sp/spr/steps_cache/html/vennplot_4adb227323bb9b1404fce13c3a059901.rdx rename to blogdown/en/sp/spr/steps_cache/html/vennplot_cd8ec7b8c4dd60491e94fd04608b7e9d.rdx diff --git a/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_7b1be5dfcface5ea02e433cbd6e2467a.RData b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_7b1be5dfcface5ea02e433cbd6e2467a.RData new file mode 100644 index 000000000..9584b42e3 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_7b1be5dfcface5ea02e433cbd6e2467a.RData differ diff --git a/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_7b1be5dfcface5ea02e433cbd6e2467a.rdb b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_7b1be5dfcface5ea02e433cbd6e2467a.rdb new file mode 100644 index 000000000..e69de29bb diff --git a/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_7b1be5dfcface5ea02e433cbd6e2467a.rdx b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_7b1be5dfcface5ea02e433cbd6e2467a.rdx new file mode 100644 index 000000000..99a1b29ad Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_7b1be5dfcface5ea02e433cbd6e2467a.rdx differ diff --git a/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_bowtiePE_61c636b3067cb0605eb1bd5e9d2c0c1e.RData b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_bowtiePE_61c636b3067cb0605eb1bd5e9d2c0c1e.RData new file mode 100644 index 000000000..bf50adb6a Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_bowtiePE_61c636b3067cb0605eb1bd5e9d2c0c1e.RData differ diff --git a/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_bowtiePE_61c636b3067cb0605eb1bd5e9d2c0c1e.rdb b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_bowtiePE_61c636b3067cb0605eb1bd5e9d2c0c1e.rdb new file mode 100644 index 000000000..e69de29bb diff --git a/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_bowtiePE_61c636b3067cb0605eb1bd5e9d2c0c1e.rdx b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_bowtiePE_61c636b3067cb0605eb1bd5e9d2c0c1e.rdx new file mode 100644 index 000000000..99a1b29ad Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_bowtiePE_61c636b3067cb0605eb1bd5e9d2c0c1e.rdx differ diff --git a/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_bwaPE_a2221721a031147c59e6274d5274d19f.RData b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_bwaPE_a2221721a031147c59e6274d5274d19f.RData new file mode 100644 index 000000000..606a73707 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_bwaPE_a2221721a031147c59e6274d5274d19f.RData differ diff --git a/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_bwaPE_a2221721a031147c59e6274d5274d19f.rdb b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_bwaPE_a2221721a031147c59e6274d5274d19f.rdb new file mode 100644 index 000000000..e69de29bb diff --git a/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_bwaPE_a2221721a031147c59e6274d5274d19f.rdx b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_bwaPE_a2221721a031147c59e6274d5274d19f.rdx new file mode 100644 index 000000000..99a1b29ad Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_bwaPE_a2221721a031147c59e6274d5274d19f.rdx differ diff --git a/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_gsnap_b50c0a298105a83432938a525e433c59.RData b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_gsnap_b50c0a298105a83432938a525e433c59.RData new file mode 100644 index 000000000..14e0414f0 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_gsnap_b50c0a298105a83432938a525e433c59.RData differ diff --git a/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_gsnap_b50c0a298105a83432938a525e433c59.rdb b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_gsnap_b50c0a298105a83432938a525e433c59.rdb new file mode 100644 index 000000000..e69de29bb diff --git a/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_gsnap_b50c0a298105a83432938a525e433c59.rdx b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_gsnap_b50c0a298105a83432938a525e433c59.rdx new file mode 100644 index 000000000..99a1b29ad Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_gsnap_b50c0a298105a83432938a525e433c59.rdx differ diff --git a/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_rsubread_72e89cfc55e78ca9eaf1ec5e518484a2.RData b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_rsubread_72e89cfc55e78ca9eaf1ec5e518484a2.RData new file mode 100644 index 000000000..a27887b23 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_rsubread_72e89cfc55e78ca9eaf1ec5e518484a2.RData differ diff --git a/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_rsubread_72e89cfc55e78ca9eaf1ec5e518484a2.rdb b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_rsubread_72e89cfc55e78ca9eaf1ec5e518484a2.rdb new file mode 100644 index 000000000..e69de29bb diff --git a/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_rsubread_72e89cfc55e78ca9eaf1ec5e518484a2.rdx b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_rsubread_72e89cfc55e78ca9eaf1ec5e518484a2.rdx new file mode 100644 index 000000000..99a1b29ad Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_rsubread_72e89cfc55e78ca9eaf1ec5e518484a2.rdx differ diff --git a/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_tophat2PE_f582295bc6f9537d2bf79b01d009ab02.RData b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_tophat2PE_f582295bc6f9537d2bf79b01d009ab02.RData new file mode 100644 index 000000000..642ff9342 Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_tophat2PE_f582295bc6f9537d2bf79b01d009ab02.RData differ diff --git a/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_tophat2PE_f582295bc6f9537d2bf79b01d009ab02.rdb b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_tophat2PE_f582295bc6f9537d2bf79b01d009ab02.rdb new file mode 100644 index 000000000..e69de29bb diff --git a/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_tophat2PE_f582295bc6f9537d2bf79b01d009ab02.rdx b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_tophat2PE_f582295bc6f9537d2bf79b01d009ab02.rdx new file mode 100644 index 000000000..99a1b29ad Binary files /dev/null and b/blogdown/en/sp/spr/steps_cache/html/writeTargetsout_tophat2PE_f582295bc6f9537d2bf79b01d009ab02.rdx differ diff --git a/blogdown/md5sum.txt b/blogdown/md5sum.txt index 24799e551..313162e60 100644 --- a/blogdown/md5sum.txt +++ b/blogdown/md5sum.txt @@ -7,19 +7,21 @@ "content/en/presentations/sps/SPS_intro.Rmd" "2dffa2488c602e1daaff2edde3eb25ec" "content/en/presentations/SPS/SPS_intro.Rmd" "2dffa2488c602e1daaff2edde3eb25ec" "content/en/sp/SP_docker.Rmd" "c6f6969d28205d0daa3939f5be85603a" +"content/en/sp/spr/cwl_and_spr.Rmd" "7a704a87f32eed9aebeb504a488ed902" +"content/en/sp/spr/cwl_syntax.Rmd" "ba601785df9ab8f776dc4107e80bba1b" "content/en/sp/spr/gettingstarted.Rmarkdown" "f2bf3b498d3bc1bd3abc5733f2e40052" "content/en/sp/SPR/gettingstarted.Rmarkdown" "f58fbedb6be2b84484cd0707adaf1736" -"content/en/sp/spr/gettingstarted.Rmd" "2987c3ebeb5f5843a020c0166657859b" +"content/en/sp/spr/gettingstarted.Rmd" "6b9cb8c3e22c627627e52eae4f2a3e36" "content/en/sp/spr/introduction.Rmarkdown" "db6ccd750b920a509a97fbe8ffdced36" "content/en/sp/SPR/introduction.Rmarkdown" "db6ccd750b920a509a97fbe8ffdced36" "content/en/sp/spr/introduction.Rmd" "892cf3d3c5d7fbc98a2e64f7d40f2cc1" -"content/en/sp/spr/SP_docker.Rmd" "bec0e2c81c6e9dac4b3e76366c2b5843" +"content/en/sp/spr/SP_docker.Rmd" "50a95cf7008fb630d13edc63ad2190a8" "content/en/sp/SPR/SP_docker.Rmd" "5610ea02695b82efb82d765646d6dc3d" "content/en/sp/spr/spr_run.Rmarkdown" "b6b58d19329135f57f7fb6a07fbf29ad" "content/en/sp/SPR/spr_run.Rmarkdown" "f5c82aa80df42ea875b63f68c3479d6d" -"content/en/sp/spr/SPRinstall.Rmarkdown" "6cd516529bbd80e97f946e6612680b09" +"content/en/sp/spr/SPRinstall.Rmarkdown" "fd1d0ebf38c3655a881fbb0e183c0d95" "content/en/sp/SPR/SPRinstall.Rmarkdown" "6cd516529bbd80e97f946e6612680b09" -"content/en/sp/spr/steps.Rmarkdown" "449b8b221732c3c94e78af965081c57d" +"content/en/sp/spr/steps.Rmarkdown" "9a78a8a956dd92ba25c4661a89b2f200" "content/en/sp/SPR/steps.Rmarkdown" "449b8b221732c3c94e78af965081c57d" "content/en/sp/spr/templates.Rmarkdown" "498f6995986f6e5c113b7d51212a40ac" "content/en/sp/SPR/templates.Rmarkdown" "498f6995986f6e5c113b7d51212a40ac" @@ -58,7 +60,7 @@ "content/en/sps/adv_features/tabs.Rmarkdown" "fe5d1c5a26323e41ef5ec6acb93e8ecd" "content/en/sps/adv_features/tabs.Rmd" "90362ef199db468ce49d09e19dca8fec" "content/en/sps/dev/_index.Rmarkdown" "fd3ea8c1242d03c38b67b7a97b7ce38c" -"content/en/sps/dev/_index.Rmd" "79a0871e20ee4372e29c5cb750d9642e" +"content/en/sps/dev/_index.Rmd" "962db203eb746c63b36e42ace811c631" "content/en/sps/dev/spscomps/server.Rmarkdown" "bbac38b3912e031093f84803cc96a3c3" "content/en/sps/dev/spscomps/server.Rmd" "bbac38b3912e031093f84803cc96a3c3" "content/en/sps/dev/spscomps/ui.Rmarkdown" "b94a428e18b0864e8617baf7ccbc30bc" diff --git a/content/en/sp/spr/.SPRproject/SYSargsList.yml b/content/en/sp/spr/.SPRproject/SYSargsList.yml deleted file mode 100644 index aeccf4663..000000000 --- a/content/en/sp/spr/.SPRproject/SYSargsList.yml +++ /dev/null @@ -1,464 +0,0 @@ -stepsWF: - newStep2: | - codeLine: - - mapply(function(x, y) write.csv(x, y), split(iris, factor(iris$Species)), file.path("results", - paste0(names(split(iris, factor(iris$Species))), ".csv"))) - - '3.91202300542815' - codeChunkStart: [] - rmdPath: [] - stepName: export_iris - dependency: - export_iris: '' - status: - status.summary: Pending - status.completed: - Step: export_iris - status.summary: Pending - status.time: {} - files: [] - newIndex: | - targets: - SE: - FileName: results/setosa.csv - SampleName: SE - VE: - FileName: results/versicolor.csv - SampleName: VE - VI: - FileName: results/virginica.csv - SampleName: VI - targetsheader: - targetsheader: '# Project ID: SPR Example gzip' - modules: [] - wf: - class: Workflow - cwlVersion: v1.0 - inputs: - file: File - SampleName: string - ext: string - results_path: Directory - outputs: - gzip_file: - outputSource: gzip/gzip_file - type: stdout - steps: - gzip: - in: - file: file - SampleName: SampleName - ext: ext - results_path: results_path - out: '[gzip_file]' - run: gunzip/gzip.cwl - clt: - gunzip/gzip.cwl: - cwlVersion: v1.0 - class: CommandLineTool - baseCommand: gzip - requirements: - - class: InlineJavascriptRequirement - - class: InitialWorkDirRequirement - listing: $(inputs.results_path) - arguments: - - prefix: -c - inputs: - file: - type: File - inputBinding: - position: 1 - SampleName: - label: Filename to write output to - type: string - ext: - label: Filename extension - type: string - results_path: - label: Directory to write output to - type: Directory - outputs: - gzip_file: - type: stdout - stdout: $(inputs.results_path.basename)/$(inputs.SampleName).$(inputs.ext) - yamlinput: - file: - class: File - path: _FILE_PATH_ - SampleName: _SampleName_ - ext: txt.gz - results_path: - class: Directory - path: ./results - cmdlist: - SE: - gzip: gzip -c results/setosa.csv > results/SE.txt.gz - VE: - gzip: gzip -c results/versicolor.csv > results/VE.txt.gz - VI: - gzip: gzip -c results/virginica.csv > results/VI.txt.gz - input: - SE: - FileName: results/setosa.csv - SampleName: SE - VE: - FileName: results/versicolor.csv - SampleName: VE - VI: - FileName: results/virginica.csv - SampleName: VI - output: - SE: - gzip: results/SE.txt.gz - VE: - gzip: results/VE.txt.gz - VI: - gzip: results/VI.txt.gz - files: - cwl: gunzip/workflow_gzip.cwl - yml: gunzip/gzip.yml - dir_path: /home/dcassol/src/R-4.1.0/library/systemPipeR/extdata/cwl - steps: gzip - cltpaths: /home/dcassol/src/R-4.1.0/library/systemPipeR/extdata/cwl/gunzip/gzip.cwl - output_names: gzip_file - targets: home/dcassol/src/R-4.1.0/library/systemPipeR/extdata/cwl/gunzip/targets_gunzip.txt - inputvars: - FileName: _FILE_PATH_ - SampleName: _SampleName_ - cmdToCwl: [] - status: - status.summary: Pending - status.completed: - Targets: - - SE - - VE - - VI - Total_Files: - - 1.0 - - 1.0 - - 1.0 - Existing_Files: - - 0.0 - - 0.0 - - 0.0 - Missing_Files: - - 1.0 - - 1.0 - - 1.0 - gzip: - - Pending - - Pending - - Pending - status.time: {} - internal_outfiles: - SE: - gzip: results/SE.txt.gz - VE: - gzip: results/VE.txt.gz - VI: - gzip: results/VI.txt.gz - gunzip: | - targets: - SE: - gzip_file: results/SE.csv.gz - SampleName: SE - VE: - gzip_file: results/VE.csv.gz - SampleName: VE - VI: - gzip_file: results/VI.csv.gz - SampleName: VI - targetsheader: - targetsheader: '# Project ID: SPR Example gzip' - modules: [] - wf: - class: Workflow - cwlVersion: v1.0 - inputs: - file: File - SampleName: string - ext: string - results_path: Directory - outputs: - gunzip_file: - outputSource: gunzip/gunzip_file - type: stdout - steps: - gunzip: - in: - file: file - SampleName: SampleName - ext: ext - results_path: results_path - out: '[gunzip_file]' - run: gunzip/gunzip.cwl - clt: - gunzip/gunzip.cwl: - cwlVersion: v1.0 - class: CommandLineTool - baseCommand: gunzip - requirements: - - class: InlineJavascriptRequirement - - class: InitialWorkDirRequirement - listing: $(inputs.results_path) - arguments: - - prefix: -c - inputs: - file: - type: File - inputBinding: - position: 1 - SampleName: - label: Filename to write output to - type: string - ext: - label: Filename extension - type: string - results_path: - label: Directory to write output to - type: Directory - outputs: - gunzip_file: - type: stdout - stdout: $(inputs.results_path.basename)/$(inputs.SampleName).csv - yamlinput: - file: - class: File - path: _FILE_PATH_ - SampleName: _SampleName_ - ext: csv - results_path: - class: Directory - path: ./results - cmdlist: - SE: - gunzip: gunzip -c results/SE.csv.gz > results/SE.csv - VE: - gunzip: gunzip -c results/VE.csv.gz > results/VE.csv - VI: - gunzip: gunzip -c results/VI.csv.gz > results/VI.csv - input: - SE: - gzip_file: results/SE.csv.gz - SampleName: SE - VE: - gzip_file: results/VE.csv.gz - SampleName: VE - VI: - gzip_file: results/VI.csv.gz - SampleName: VI - output: - SE: - gunzip: results/SE.csv - VE: - gunzip: results/VE.csv - VI: - gunzip: results/VI.csv - files: - cwl: gunzip/workflow_gunzip.cwl - yml: gunzip/gunzip.yml - dir_path: /home/dcassol/src/R-4.1.0/library/systemPipeR/extdata/cwl - steps: gunzip - cltpaths: /home/dcassol/src/R-4.1.0/library/systemPipeR/extdata/cwl/gunzip/gunzip.cwl - output_names: gunzip_file - targets: .na - inputvars: - gzip_file: _FILE_PATH_ - SampleName: _SampleName_ - cmdToCwl: [] - status: - status.summary: Pending - status.completed: - Targets: - - SE - - VE - - VI - Total_Files: - - 1.0 - - 1.0 - - 1.0 - Existing_Files: - - 0.0 - - 0.0 - - 0.0 - Missing_Files: - - 1.0 - - 1.0 - - 1.0 - gunzip: - - Pending - - Pending - - Pending - status.time: {} - internal_outfiles: - SE: - gunzip: results/SE.csv - VE: - gunzip: results/VE.csv - VI: - gunzip: results/VI.csv - iris_stats: | - codeLine: - - df <- lapply(getColumn(sal, step = "gunzip", "outfiles"), function(x) read.delim(x, - sep = ",")[-1]) - - df <- do.call(rbind, df) - - stats <- data.frame(cbind(mean = apply(df[, 1:4], 2, mean), sd = apply(df[, 1:4], - 2, sd))) - - stats$species <- rownames(stats) - - plot <- ggplot2::ggplot(stats, ggplot2::aes(x = species, y = mean, fill = species)) - + ggplot2::geom_bar(stat = "identity", color = "black", position = ggplot2::position_dodge()) - + ggplot2::geom_errorbar(ggplot2::aes(ymin = mean - sd, ymax = mean + sd), width - = 0.2, position = ggplot2::position_dodge(0.9)) - codeChunkStart: [] - rmdPath: [] - stepName: iris_stats - dependency: - iris_stats: gzip - status: - status.summary: Pending - status.completed: - Step: iris_stats - status.summary: Pending - status.time: {} - files: [] -statusWF: - newStep2: | - newStep2: - status.summary: Pending - status.completed: - Step: export_iris - status.summary: Pending - status.time: {} - newIndex: | - newIndex: - status.summary: Pending - status.completed: - Targets: - - SE - - VE - - VI - Total_Files: - - 1.0 - - 1.0 - - 1.0 - Existing_Files: - - 0.0 - - 0.0 - - 0.0 - Missing_Files: - - 1.0 - - 1.0 - - 1.0 - gzip: - - Pending - - Pending - - Pending - status.time: {} - gunzip: | - gunzip: - status.summary: Pending - status.completed: - Targets: - - SE - - VE - - VI - Total_Files: - - 1.0 - - 1.0 - - 1.0 - Existing_Files: - - 0.0 - - 0.0 - - 0.0 - Missing_Files: - - 1.0 - - 1.0 - - 1.0 - gunzip: - - Pending - - Pending - - Pending - status.time: {} - iris_stats: | - iris_stats: - status.summary: Pending - status.completed: - Step: iris_stats - status.summary: Pending - status.time: {} -targetsWF: - newStep2: | - {} - newIndex: | - FileName: - - results/setosa.csv - - results/versicolor.csv - - results/virginica.csv - SampleName: - - SE - - VE - - VI - gunzip: | - gzip_file: - - results/SE.csv.gz - - results/VE.csv.gz - - results/VI.csv.gz - SampleName: - - SE - - VE - - VI - iris_stats: | - {} -outfiles: - newStep2: | - {} - newIndex: | - gzip_file: - - results/SE.csv.gz - - results/VE.csv.gz - - results/VI.csv.gz - gunzip: | - gunzip_file: - - results/SE.csv - - results/VE.csv - - results/VI.csv - iris_stats: | - {} -SEobj: | - [] -dependency: - newStep2: | - newStep2: '' - newIndex: | - newIndex: newStep2 - gunzip: | - gunzip: newIndex - iris_stats: | - iris_stats: newIndex -targets_connection: - newStep2: | - newStep2: ~ - newIndex: | - newIndex: ~ - gunzip: | - gunzip: - targets_step: newIndex - new_targets_col: - new_targets_col: - - gzip_file - - SampleName - rm_targets_col: - rm_targets_col: FileName - iris_stats: | - iris_stats: ~ -projectInfo: | - project: /home/dcassol/danielac@ucr.edu/projects/SP/SPR_org/systemPipeR.github.io_docsy/content/en/sp/spr - data: data - param: param - results: results - logsDir: .SPRproject - sysargslist: .SPRproject/SYSargsList.yml -runInfo: | - newStep2: no - newIndex: yes - gunzip: yes - iris_stats: no diff --git a/content/en/sp/spr/.~1EMZjOx0kYtHjoPe-rLWT8TepMqa4-3lg-60623e.insyncdl b/content/en/sp/spr/.~1EMZjOx0kYtHjoPe-rLWT8TepMqa4-3lg-60623e.insyncdl new file mode 100644 index 000000000..e69de29bb diff --git a/content/en/sp/spr/SPRinstall.Rmarkdown b/content/en/sp/spr/SPRinstall.Rmarkdown index 1889f8e6c..ddd338e0f 100644 --- a/content/en/sp/spr/SPRinstall.Rmarkdown +++ b/content/en/sp/spr/SPRinstall.Rmarkdown @@ -16,7 +16,7 @@ bibliography: bibtex_install.bib editor_options: chunk_output_type: console type: docs -weight: 7 +weight: 8 --- ```{css, echo=FALSE} @@ -48,11 +48,10 @@ suppressPackageStartupMessages({ }) ``` -# - ## `systemPipeR` Installation -To install the `systemPipeR` package [@H_Backman2016-bt], please use the _`BiocManager::install`_ command: +To install the `systemPipeR` package [@H_Backman2016-bt], please use +the _`BiocManager::install`_ command: ```{r spr_install, eval=FALSE} if (!requireNamespace("BiocManager", quietly=TRUE)) @@ -61,57 +60,34 @@ BiocManager::install("systemPipeR") ``` To obtain the most recent updates immediately, one can install it directly from -[github](https://github.com/tgirke/systemPipeR) as follow: +[GitHub](https://github.com/tgirke/systemPipeR) as follow: ```{r spr_install_gh, eval=FALSE} if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") -BiocManager::install("tgirke/systemPipeR", build_vignettes=TRUE, dependencies=TRUE) +BiocManager::install("tgirke/systemPipeR", dependencies=TRUE) ``` ## Third-party software tools in *`SPR`* -This guide provides detailed installation instructions for the software tools used within `systemPipeR` package. This guide provides the instruction for a Linux system. - -### BWA - -[Burrow-Wheeler Aligner (BWA)](https://github.com/lh3/bwa) for short-read alignment [@Li2013-sw]. - -```{bash bwa, eval=FALSE} -git clone https://github.com/lh3/bwa.git -cd bwa -make -vim ~/.bashrc ## Open the Bash shell script -export PATH=$PATH:/path/to/bwa ## "/path/to/bwa" is an example! Replace with real PATH -source ~/.bashrc -bwa ## Test if the installation was successful -``` - -Note: In some systems, `~/.bash_profile` is used in place of `~/.bashrc`. - -More information about how to set an enviroment variable [here](https://en.wikipedia.org/wiki/Environment_variable). - -### BLAST - -Please check the [BLAST Command Line Applications User Manual](https://www.ncbi.nlm.nih.gov/books/NBK279671/) to -find the installation introduction for your system environment. - -Download the latest version from [here](https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/), as the following example: - -```{bash blast, eval=FALSE} -wget https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.11.0+-x64-linux.tar.gz -tar zxvpf ncbi-blast-2.11.0+-x64-linux.tar.gz ncbi-blast-2.11.0+/ -cd ncbi-blast-2.11.0+/ -export PATH=$PATH:/path/to//ncbi-blast-2.11.0+/bin ## "/path/to/ncbi-blast-2.11.0+" is an example! Replace with real PATH -``` - -### Cutadapt - -Please check the [Cutadapt Manual](https://cutadapt.readthedocs.io/en/stable/installation.html) to -find the installation introduction for your system environment. - -```{bash Cutadapt, eval=FALSE} -sudo apt install cutadapt +Current, *systemPipeR* provides the _`param`_ file templates for third-party +software tools. Please check the listed software tools. + +```{r table_tools, echo=FALSE, message=FALSE} +library(magrittr) +SPR_software <- system.file("extdata", "SPR_software.csv", package = "systemPipeR") +software <- read.delim(SPR_software, sep = ",", comment.char = "#") +colors <- colorRampPalette((c("darkseagreen", "indianred1")))(length(unique(software$Category))) +id <- as.numeric(c((unique(software$Category)))) +software %>% + dplyr::mutate(Step = kableExtra::cell_spec(Step, color = "white", bold = TRUE, + background = factor(Category, id, colors) + )) %>% + dplyr::select(Tool, Description, Step) %>% + dplyr::arrange(Tool) %>% + kableExtra::kable(escape = FALSE, align = "c", col.names = c("Tool Name", "Description", "Step")) %>% + kableExtra::kable_styling(c("striped", "hover", "condensed"), full_width = TRUE) %>% + kableExtra::scroll_box(width = "100%", height = "500px") ``` ## References diff --git a/content/en/sp/spr/SPRinstall.markdown b/content/en/sp/spr/SPRinstall.markdown index 127982e0b..32b880aba 100644 --- a/content/en/sp/spr/SPRinstall.markdown +++ b/content/en/sp/spr/SPRinstall.markdown @@ -1,7 +1,7 @@ --- -title: "SPR detailed installation instructions" +title: "SPR detailed installation instructions" author: "Author: Daniela Cassol (danicassol@gmail.com)" -date: "Last update: 20 April, 2021" +date: "Last update: 28 October, 2021" output: BiocStyle::html_document: toc_float: true @@ -13,12 +13,16 @@ vignette: | %\VignetteEngine{knitr::rmarkdown} fontsize: 14pt bibliography: bibtex_install.bib -editor_options: +editor_options: chunk_output_type: console type: docs -weight: 7 +weight: 8 --- + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - -systemPipeR 1.27.21
- -A typical workflow starts with generating the expected working environment
-containing the proper directory structure, input files, and parameter settings.
-To simplify this task, one can load one of the existing NGS workflows templates
-provided by systemPipeRdata
into the current working directory. The
-following does this for the rnaseq
template. The name of the resulting
-workflow directory can be specified under the mydirname
argument. The
-default NULL
uses the name of the chosen workflow. An error is issued if a
-directory of the same name and path exists already. On Linux and OS X systems
-one can also create new workflow instances from the command-line of a terminal as shown
-here.
-To apply workflows to custom data, the user needs to modify the targets
file and if
-necessary update the corresponding .cwl
and .yml
files. A collection of pre-generated .cwl
and .yml
files are provided in the param/cwl
subdirectory of each workflow template. They
-are also viewable in the GitHub repository of systemPipeRdata
(see
-here).
library(systemPipeR)
-library(systemPipeRdata)
-genWorkenvir(workflow = "rnaseq", mydirname = NULL)
-setwd("rnaseq")
-preprocessReads
functionThe function preprocessReads
allows to apply predefined or custom
-read preprocessing functions to all FASTQ files referenced in a
-SYSargs2
container, such as quality filtering or adaptor trimming
-routines. The paths to the resulting output FASTQ files are stored in the
-output
slot of the SYSargs2
object. Internally,
-preprocessReads
uses the FastqStreamer
function from
-the ShortRead
package to stream through large FASTQ files in a
-memory-efficient manner. The following example performs adaptor trimming with
-the trimLRPatterns
function from the Biostrings
package.
-After the trimming step a new targets file is generated (here
-targets_trimPE.txt
) containing the paths to the trimmed FASTQ files.
-The new targets file can be used for the next workflow step with an updated
-SYSargs2
instance, e.g. running the NGS alignments with the
-trimmed FASTQ files.
Construct SYSargs2
object from cwl
and yml
param and targets
files.
targetsPE <- system.file("extdata", "targetsPE.txt", package = "systemPipeR")
-dir_path <- system.file("extdata/cwl/preprocessReads/trim-pe", package = "systemPipeR")
-trim <- loadWorkflow(targets = targetsPE, wf_file = "trim-pe.cwl", input_file = "trim-pe.yml",
- dir_path = dir_path)
-trim <- renderWF(trim, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_",
- SampleName = "_SampleName_"))
-trim
-output(trim)[1:2]
-preprocessReads(args = trim, Fct = "trimLRPatterns(Rpattern='GCCCGGGTAA',
- subject=fq)",
- batchsize = 1e+05, overwrite = TRUE, compress = TRUE)
-The following example shows how one can design a custom read preprocessing function
-using utilities provided by the ShortRead
package, and then run it
-in batch mode with the ‘preprocessReads’ function (here on paired-end reads).
filterFct <- function(fq, cutoff = 20, Nexceptions = 0) {
- qcount <- rowSums(as(quality(fq), "matrix") <= cutoff, na.rm = TRUE)
- # Retains reads where Phred scores are >= cutoff with N exceptions
- fq[qcount <= Nexceptions]
-}
-preprocessReads(args = trim, Fct = "filterFct(fq, cutoff=20, Nexceptions=0)", batchsize = 1e+05)
-TrimGalore! is -a wrapper tool to consistently apply quality and adapter trimming to fastq files, -with some extra functionality for removing Reduced Representation Bisulfite-Seq -(RRBS) libraries.
-targets <- system.file("extdata", "targets.txt", package = "systemPipeR")
-dir_path <- system.file("extdata/cwl/trim_galore/trim_galore-se", package = "systemPipeR")
-trimG <- loadWorkflow(targets = targets, wf_file = "trim_galore-se.cwl", input_file = "trim_galore-se.yml",
- dir_path = dir_path)
-trimG <- renderWF(trimG, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
-trimG
-cmdlist(trimG)[1:2]
-output(trimG)[1:2]
-## Run Single Machine Option
-trimG <- runCommandline(trimG[1], make_bam = FALSE)
-targetsPE <- system.file("extdata", "targetsPE.txt", package = "systemPipeR")
-dir_path <- system.file("extdata/cwl/trimmomatic/trimmomatic-pe", package = "systemPipeR")
-trimM <- loadWorkflow(targets = targetsPE, wf_file = "trimmomatic-pe.cwl", input_file = "trimmomatic-pe.yml",
- dir_path = dir_path)
-trimM <- renderWF(trimM, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_",
- SampleName = "_SampleName_"))
-trimM
-cmdlist(trimM)[1:2]
-output(trimM)[1:2]
-## Run Single Machine Option
-trimM <- runCommandline(trimM[1], make_bam = FALSE)
-The following seeFastq
and seeFastqPlot
functions generate and plot a series of
-useful quality statistics for a set of FASTQ files including per cycle quality
-box plots, base proportions, base-level quality trends, relative k-mer
-diversity, length and occurrence distribution of reads, number of reads above
-quality cutoffs and mean quality distribution.
-The function seeFastq
computes the quality statistics and stores the results in a
-relatively small list object that can be saved to disk with save()
and
-reloaded with load()
for later plotting. The argument klength
specifies the
-k-mer length and batchsize
the number of reads to a random sample from each
-FASTQ file.
fqlist <- seeFastq(fastq = infile1(trim), batchsize = 10000, klength = 8)
-pdf("./results/fastqReport.pdf", height = 18, width = 4 * length(fqlist))
-seeFastqPlot(fqlist)
-dev.off()
-Parallelization of FASTQ quality report on a single machine with multiple cores.
-f <- function(x) seeFastq(fastq = infile1(trim)[x], batchsize = 1e+05, klength = 8)
-fqlist <- bplapply(seq(along = trim), f, BPPARAM = MulticoreParam(workers = 4))
-seeFastqPlot(unlist(fqlist, recursive = FALSE))
-Parallelization of FASTQ quality report via scheduler (e.g. Slurm) across several compute nodes.
-library(BiocParallel)
-library(batchtools)
-f <- function(x) {
- library(systemPipeR)
- targetsPE <- system.file("extdata", "targetsPE.txt", package = "systemPipeR")
- dir_path <- system.file("extdata/cwl/preprocessReads/trim-pe", package = "systemPipeR")
- trim <- loadWorkflow(targets = targetsPE, wf_file = "trim-pe.cwl", input_file = "trim-pe.yml",
- dir_path = dir_path)
- trim <- renderWF(trim, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_",
- SampleName = "_SampleName_"))
- seeFastq(fastq = infile1(trim)[x], batchsize = 1e+05, klength = 8)
-}
-resources <- list(walltime = 120, ntasks = 1, ncpus = 4, memory = 1024)
-param <- BatchtoolsParam(workers = 4, cluster = "slurm", template = "batchtools.slurm.tmpl",
- resources = resources)
-fqlist <- bplapply(seq(along = trim), f, BPPARAM = param)
-seeFastqPlot(unlist(fqlist, recursive = FALSE))
-After quality control, the sequence reads can be aligned to a reference genome or -transcriptome database. The following sessions present some NGS sequence alignment -software. Select the most accurate aligner and determining the optimal parameter -for your custom data set project.
-For all the following examples, it is necessary to install the respective software
-and export the PATH
accordingly. If it is available Environment Module
-in the system, you can load all the request software with moduleload(args)
function.
HISAT2
using SYSargs2
The following steps will demonstrate how to use the short read aligner Hisat2
-(Kim, Langmead, and Salzberg 2015) in both interactive job submissions and batch submissions to
-queuing systems of clusters using the systemPipeR's
new CWL command-line interface.
The parameter settings of the aligner are defined in the hisat2-mapping-se.cwl
-and hisat2-mapping-se.yml
files. The following shows how to construct the
-corresponding SYSargs2 object, here args.
targets <- system.file("extdata", "targets.txt", package = "systemPipeR")
-dir_path <- system.file("extdata/cwl/hisat2/hisat2-se", package = "systemPipeR")
-args <- loadWorkflow(targets = targets, wf_file = "hisat2-mapping-se.cwl", input_file = "hisat2-mapping-se.yml",
- dir_path = dir_path)
-args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
-args
-## Instance of 'SYSargs2':
-## Slot names/accessors:
-## targets: 18 (M1A...V12B), targetsheader: 4 (lines)
-## modules: 1
-## wf: 0, clt: 1, yamlinput: 7 (inputs)
-## input: 18, output: 18
-## cmdlist: 18
-## Sub Steps:
-## 1. hisat2-mapping-se (rendered: TRUE)
-cmdlist(args)[1:2]
-## $M1A
-## $M1A$`hisat2-mapping-se`
-## [1] "hisat2 -S ./results/M1A.sam -x ./data/tair10.fasta -k 1 --min-intronlen 30 --max-intronlen 3000 -U ./data/SRR446027_1.fastq.gz --threads 4"
-##
-##
-## $M1B
-## $M1B$`hisat2-mapping-se`
-## [1] "hisat2 -S ./results/M1B.sam -x ./data/tair10.fasta -k 1 --min-intronlen 30 --max-intronlen 3000 -U ./data/SRR446028_1.fastq.gz --threads 4"
-output(args)[1:2]
-## $M1A
-## $M1A$`hisat2-mapping-se`
-## [1] "./results/M1A.sam"
-##
-##
-## $M1B
-## $M1B$`hisat2-mapping-se`
-## [1] "./results/M1B.sam"
-Subsetting SYSargs2
class slots for each workflow step.
subsetWF(args, slot = "input", subset = "FileName")[1:2] ## Subsetting the input files for this particular workflow
-## M1A M1B
-## "./data/SRR446027_1.fastq.gz" "./data/SRR446028_1.fastq.gz"
-subsetWF(args, slot = "output", subset = 1, index = 1)[1:2] ## Subsetting the output files for one particular step in the workflow
-## M1A M1B
-## "./results/M1A.sam" "./results/M1B.sam"
-subsetWF(args, slot = "step", subset = 1)[1] ## Subsetting the command-lines for one particular step in the workflow
-## M1A
-## "hisat2 -S ./results/M1A.sam -x ./data/tair10.fasta -k 1 --min-intronlen 30 --max-intronlen 3000 -U ./data/SRR446027_1.fastq.gz --threads 4"
-subsetWF(args, slot = "output", subset = 1, index = 1, delete = TRUE)[1] ## DELETING specific output files
-## The subset cannot be deleted: no such file
-## M1A
-## "./results/M1A.sam"
-Build Hisat2
index.
dir_path <- system.file("extdata/cwl/hisat2/hisat2-idx", package = "systemPipeR")
-idx <- loadWorkflow(targets = NULL, wf_file = "hisat2-index.cwl", input_file = "hisat2-index.yml",
- dir_path = dir_path)
-idx <- renderWF(idx)
-idx
-cmdlist(idx)
-
-## Run
-runCommandline(idx, make_bam = FALSE)
-To simplify the short read alignment execution for the user, the command-line
-can be run with the runCommandline
function.
-The execution will be on a single machine without submitting to a queuing system
-of a computer cluster. This way, the input FASTQ files will be processed sequentially.
-By default runCommandline
auto detects SAM file outputs and converts them
-to sorted and indexed BAM files, using internally the Rsamtools
package
-(Morgan et al. 2019). Besides, runCommandline
allows the user to create a dedicated
-results folder for each workflow and a sub-folder for each sample
-defined in the targets file. This includes all the output and log files for each
-step. When these options are used, the output location will be updated by default
-and can be assigned to the same object.
runCommandline(args, make_bam = FALSE) ## generates alignments and writes *.sam files to ./results folder
-args <- runCommandline(args, make_bam = TRUE) ## same as above but writes files and converts *.sam files to sorted and indexed BAM files. Assigning the new extention of the output files to the object args.
-If available, multiple CPU cores can be used for processing each file. The number
-of CPU cores (here 4) to use for each process is defined in the *.yml
file.
-With yamlinput(args)['thread']
one can return this value from the SYSargs2
object.
Alternatively, the computation can be greatly accelerated by processing many files
-in parallel using several compute nodes of a cluster, where a scheduling/queuing
-system is used for load balancing. For this the clusterRun
function submits
-the computing requests to the scheduler using the run specifications
-defined by runCommandline
.
To avoid over-subscription of CPU cores on the compute nodes, the value from
-yamlinput(args)['thread']
is passed on to the submission command, here ncpus
-in the resources
list object. The number of independent parallel cluster
-processes is defined under the Njobs
argument. The following example will run
-18 processes in parallel using for each 4 CPU cores. If the resources available
-on a cluster allow running all 18 processes at the same time then the shown sample
-submission will utilize in total 72 CPU cores. Note, clusterRun
can be used
-with most queueing systems as it is based on utilities from the batchtools
-package which supports the use of template files (*.tmpl
) for defining the
-run parameters of different schedulers. To run the following code, one needs to
-have both a conf file (see .batchtools.conf.R
samples here)
-and a template file (see *.tmpl
samples here)
-for the queueing available on a system. The following example uses the sample
-conf and template files for the Slurm scheduler provided by this package.
library(batchtools)
-resources <- list(walltime = 120, ntasks = 1, ncpus = 4, memory = 1024)
-reg <- clusterRun(args, FUN = runCommandline, more.args = list(args = args, make_bam = TRUE,
- dir = FALSE), conffile = ".batchtools.conf.R", template = "batchtools.slurm.tmpl",
- Njobs = 18, runid = "01", resourceList = resources)
-getStatus(reg = reg)
-waitForJobs(reg = reg)
-Check and update the output location if necessary.
-args <- output_update(args, dir = FALSE, replace = TRUE, extension = c(".sam", ".bam")) ## Updates the output(args) to the right location in the subfolders
-output(args)
-To establish the connectivity to the next workflow step, one can write a new
-targets file with the writeTargetsout
function. The new targets file
-serves as input to the next loadWorkflow
and renderWF
call.
names(clt(args))
-writeTargetsout(x = args, file = "default", step = 1, new_col = "FileName", new_col_output_index = 1,
- overwrite = TRUE)
-HISAT2
and SAMtools
Alternatively, it possible to build an workflow with HISAT2
and SAMtools
.
targets <- system.file("extdata", "targets.txt", package = "systemPipeR")
-dir_path <- system.file("extdata/cwl/workflow-hisat2/workflow-hisat2-se", package = "systemPipeR")
-WF <- loadWorkflow(targets = targets, wf_file = "workflow_hisat2-se.cwl", input_file = "workflow_hisat2-se.yml",
- dir_path = dir_path)
-WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
-WF
-cmdlist(WF)[1:2]
-output(WF)[1:2]
-Tophat2
The NGS reads of this project can also be aligned against the reference genome
-sequence using Bowtie2/TopHat2
(Kim et al. 2013; Langmead and Salzberg 2012).
Build Bowtie2
index.
dir_path <- system.file("extdata/cwl/bowtie2/bowtie2-idx", package = "systemPipeR")
-idx <- loadWorkflow(targets = NULL, wf_file = "bowtie2-index.cwl", input_file = "bowtie2-index.yml",
- dir_path = dir_path)
-idx <- renderWF(idx)
-idx
-cmdlist(idx)
-
-## Run in single machine
-runCommandline(idx, make_bam = FALSE)
-The parameter settings of the aligner are defined in the tophat2-mapping-pe.cwl
-and tophat2-mapping-pe.yml
files. The following shows how to construct the
-corresponding SYSargs2 object, here tophat2PE.
targetsPE <- system.file("extdata", "targetsPE.txt", package = "systemPipeR")
-dir_path <- system.file("extdata/cwl/tophat2/tophat2-pe", package = "systemPipeR")
-tophat2PE <- loadWorkflow(targets = targetsPE, wf_file = "tophat2-mapping-pe.cwl",
- input_file = "tophat2-mapping-pe.yml", dir_path = dir_path)
-tophat2PE <- renderWF(tophat2PE, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_",
- SampleName = "_SampleName_"))
-tophat2PE
-cmdlist(tophat2PE)[1:2]
-output(tophat2PE)[1:2]
-
-## Run in single machine
-tophat2PE <- runCommandline(tophat2PE[1], make_bam = TRUE)
-Parallelization on clusters.
-resources <- list(walltime = 120, ntasks = 1, ncpus = 4, memory = 1024)
-reg <- clusterRun(tophat2PE, FUN = runCommandline, more.args = list(args = tophat2PE,
- make_bam = TRUE, dir = FALSE), conffile = ".batchtools.conf.R", template = "batchtools.slurm.tmpl",
- Njobs = 18, runid = "01", resourceList = resources)
-waitForJobs(reg = reg)
-Create new targets file
-names(clt(tophat2PE))
-writeTargetsout(x = tophat2PE, file = "default", step = 1, new_col = "tophat2PE",
- new_col_output_index = 1, overwrite = TRUE)
-Bowtie2
(e.g. for miRNA profiling)The following example runs Bowtie2
as a single process without submitting it to a cluster.
Building the index:
-dir_path <- system.file("extdata/cwl/bowtie2/bowtie2-idx", package = "systemPipeR")
-idx <- loadWorkflow(targets = NULL, wf_file = "bowtie2-index.cwl", input_file = "bowtie2-index.yml",
- dir_path = dir_path)
-idx <- renderWF(idx)
-idx
-cmdlist(idx)
-
-## Run in single machine
-runCommandline(idx, make_bam = FALSE)
-Building all the command-line:
-targetsPE <- system.file("extdata", "targetsPE.txt", package = "systemPipeR")
-dir_path <- system.file("extdata/cwl/bowtie2/bowtie2-pe", package = "systemPipeR")
-bowtiePE <- loadWorkflow(targets = targetsPE, wf_file = "bowtie2-mapping-pe.cwl",
- input_file = "bowtie2-mapping-pe.yml", dir_path = dir_path)
-bowtiePE <- renderWF(bowtiePE, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_",
- SampleName = "_SampleName_"))
-bowtiePE
-cmdlist(bowtiePE)[1:2]
-output(bowtiePE)[1:2]
-Running all the jobs to computing nodes.
-resources <- list(walltime = 120, ntasks = 1, ncpus = 4, memory = 1024)
-reg <- clusterRun(bowtiePE, FUN = runCommandline, more.args = list(args = bowtiePE,
- dir = FALSE), conffile = ".batchtools.conf.R", template = "batchtools.slurm.tmpl",
- Njobs = 18, runid = "01", resourceList = resources)
-getStatus(reg = reg)
-Alternatively, it possible to run all the jobs in a single machine.
-bowtiePE <- runCommandline(bowtiePE)
-Create new targets file.
-names(clt(bowtiePE))
-writeTargetsout(x = bowtiePE, file = "default", step = 1, new_col = "bowtiePE", new_col_output_index = 1,
- overwrite = TRUE)
-BWA-MEM
(e.g. for VAR-Seq)The following example runs BWA-MEM as a single process without submitting it to a cluster. ##TODO: add reference
-Build the index:
-dir_path <- system.file("extdata/cwl/bwa/bwa-idx", package = "systemPipeR")
-idx <- loadWorkflow(targets = NULL, wf_file = "bwa-index.cwl", input_file = "bwa-index.yml",
- dir_path = dir_path)
-idx <- renderWF(idx)
-idx
-cmdlist(idx) # Indexes reference genome
-
-## Run
-runCommandline(idx, make_bam = FALSE)
-Running the alignment:
-targetsPE <- system.file("extdata", "targetsPE.txt", package = "systemPipeR")
-dir_path <- system.file("extdata/cwl/bwa/bwa-pe", package = "systemPipeR")
-bwaPE <- loadWorkflow(targets = targetsPE, wf_file = "bwa-pe.cwl", input_file = "bwa-pe.yml",
- dir_path = dir_path)
-bwaPE <- renderWF(bwaPE, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_",
- SampleName = "_SampleName_"))
-bwaPE
-cmdlist(bwaPE)[1:2]
-output(bwaPE)[1:2]
-## Single Machine
-bwaPE <- runCommandline(args = bwaPE, make_bam = FALSE)
-
-## Cluster
-library(batchtools)
-resources <- list(walltime = 120, ntasks = 1, ncpus = 4, memory = 1024)
-reg <- clusterRun(bwaPE, FUN = runCommandline, more.args = list(args = bwaPE, dir = FALSE),
- conffile = ".batchtools.conf.R", template = "batchtools.slurm.tmpl", Njobs = 18,
- runid = "01", resourceList = resources)
-getStatus(reg = reg)
-Create new targets file.
-names(clt(bwaPE))
-writeTargetsout(x = bwaPE, file = "default", step = 1, new_col = "bwaPE", new_col_output_index = 1,
- overwrite = TRUE)
-Rsubread
(e.g. for RNA-Seq)The following example shows how one can use within the environment the R-based aligner , allowing running from R or command-line.
-## Build the index:
-dir_path <- system.file("extdata/cwl/rsubread/rsubread-idx", package = "systemPipeR")
-idx <- loadWorkflow(targets = NULL, wf_file = "rsubread-index.cwl", input_file = "rsubread-index.yml",
- dir_path = dir_path)
-idx <- renderWF(idx)
-idx
-cmdlist(idx)
-runCommandline(args = idx, make_bam = FALSE)
-
-## Running the alignment:
-targets <- system.file("extdata", "targets.txt", package = "systemPipeR")
-dir_path <- system.file("extdata/cwl/rsubread/rsubread-se", package = "systemPipeR")
-rsubread <- loadWorkflow(targets = targets, wf_file = "rsubread-mapping-se.cwl",
- input_file = "rsubread-mapping-se.yml", dir_path = dir_path)
-rsubread <- renderWF(rsubread, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
-rsubread
-cmdlist(rsubread)[1]
-
-## Single Machine
-rsubread <- runCommandline(args = rsubread[1])
-Create new targets file.
-names(clt(rsubread))
-writeTargetsout(x = rsubread, file = "default", step = 1, new_col = "rsubread", new_col_output_index = 1,
- overwrite = TRUE)
-gsnap
(e.g. for VAR-Seq and RNA-Seq)Another R-based short read aligner is gsnap
from the gmapR
package (Wu and Nacu 2010).
-The code sample below introduces how to run this aligner on multiple nodes of a compute cluster.
## Build the index:
-dir_path <- system.file("extdata/cwl/gsnap/gsnap-idx", package = "systemPipeR")
-idx <- loadWorkflow(targets = NULL, wf_file = "gsnap-index.cwl", input_file = "gsnap-index.yml",
- dir_path = dir_path)
-idx <- renderWF(idx)
-idx
-cmdlist(idx)
-runCommandline(args = idx, make_bam = FALSE)
-
-## Running the alignment:
-targetsPE <- system.file("extdata", "targetsPE.txt", package = "systemPipeR")
-dir_path <- system.file("extdata/cwl/gsnap/gsnap-pe", package = "systemPipeR")
-gsnap <- loadWorkflow(targets = targetsPE, wf_file = "gsnap-mapping-pe.cwl", input_file = "gsnap-mapping-pe.yml",
- dir_path = dir_path)
-gsnap <- renderWF(gsnap, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_",
- SampleName = "_SampleName_"))
-gsnap
-cmdlist(gsnap)[1]
-output(gsnap)[1]
-
-## Cluster
-library(batchtools)
-resources <- list(walltime = 120, ntasks = 1, ncpus = 4, memory = 1024)
-reg <- clusterRun(gsnap, FUN = runCommandline, more.args = list(args = gsnap, make_bam = FALSE),
- conffile = ".batchtools.conf.R", template = "batchtools.slurm.tmpl", Njobs = 18,
- runid = "01", resourceList = resources)
-getStatus(reg = reg)
-gsnap <- output_update(gsnap, dir = FALSE, replace = TRUE, extension = c(".sam",
- ".bam"))
-Create new targets file.
-names(clt(gsnap))
-writeTargetsout(x = gsnap, file = "default", step = 1, new_col = "gsnap", new_col_output_index = 1,
- overwrite = TRUE)
-The genome browser IGV supports reading of indexed/sorted BAM files via web URLs. This way it can be avoided to create unnecessary copies of these large files. To enable this approach, an HTML directory with Http access needs to be available in the user account (e.g. home/publichtml
) of a system. If this is not the case then the BAM files need to be moved or copied to the system where IGV runs. In the following, htmldir
defines the path to the HTML directory with http access where the symbolic links to the BAM files will be stored. The corresponding URLs will be written to a text file specified under the _urlfile
_ argument.
symLink2bam(sysargs = args, htmldir = c("~/.html/", "somedir/"), urlbase = "http://myserver.edu/~username/",
- urlfile = "IGVurl.txt")
-Create txdb
(needs to be done only once).
library(GenomicFeatures)
-txdb <- makeTxDbFromGFF(file = "data/tair10.gff", format = "gff", dataSource = "TAIR",
- organism = "Arabidopsis thaliana")
-saveDb(txdb, file = "./data/tair10.sqlite")
-The following performs read counting with summarizeOverlaps
in parallel mode with multiple cores.
library(BiocParallel)
-txdb <- loadDb("./data/tair10.sqlite")
-eByg <- exonsBy(txdb, by = "gene")
-outpaths <- subsetWF(args, slot = "output", subset = 1, index = 1)
-bfl <- BamFileList(outpaths, yieldSize = 50000, index = character())
-multicoreParam <- MulticoreParam(workers = 4)
-register(multicoreParam)
-registered()
-counteByg <- bplapply(bfl, function(x) summarizeOverlaps(eByg, x, mode = "Union",
- ignore.strand = TRUE, inter.feature = TRUE, singleEnd = TRUE))
-
-# Note: for strand-specific RNA-Seq set 'ignore.strand=FALSE' and for PE data
-# set 'singleEnd=FALSE'
-countDFeByg <- sapply(seq(along = counteByg), function(x) assays(counteByg[[x]])$counts)
-rownames(countDFeByg) <- names(rowRanges(counteByg[[1]]))
-colnames(countDFeByg) <- names(bfl)
-rpkmDFeByg <- apply(countDFeByg, 2, function(x) returnRPKM(counts = x, ranges = eByg))
-write.table(countDFeByg, "results/countDFeByg.xls", col.names = NA, quote = FALSE,
- sep = "\t")
-write.table(rpkmDFeByg, "results/rpkmDFeByg.xls", col.names = NA, quote = FALSE,
- sep = "\t")
-Please note, in addition to read counts this step generates RPKM normalized expression values. For most statistical differential expression or abundance analysis methods, such as edgeR
or DESeq2
, the raw count values should be used as input. The usage of RPKM values should be restricted to specialty applications required by some users, e.g. manually comparing the expression levels of different genes or features.
Read counting with summarizeOverlaps
using multiple nodes of a cluster.
library(BiocParallel)
-f <- function(x) {
- library(systemPipeR)
- library(BiocParallel)
- library(GenomicFeatures)
- txdb <- loadDb("./data/tair10.sqlite")
- eByg <- exonsBy(txdb, by = "gene")
- args <- systemArgs(sysma = "param/tophat.param", mytargets = "targets.txt")
- outpaths <- subsetWF(args, slot = "output", subset = 1, index = 1)
- bfl <- BamFileList(outpaths, yieldSize = 50000, index = character())
- summarizeOverlaps(eByg, bfl[x], mode = "Union", ignore.strand = TRUE, inter.feature = TRUE,
- singleEnd = TRUE)
-}
-resources <- list(walltime = 120, ntasks = 1, ncpus = 4, memory = 1024)
-param <- BatchtoolsParam(workers = 4, cluster = "slurm", template = "batchtools.slurm.tmpl",
- resources = resources)
-counteByg <- bplapply(seq(along = args), f, BPPARAM = param)
-countDFeByg <- sapply(seq(along = counteByg), function(x) assays(counteByg[[x]])$counts)
-rownames(countDFeByg) <- names(rowRanges(counteByg[[1]]))
-colnames(countDFeByg) <- names(outpaths)
-Useful commands for monitoring the progress of submitted jobs
-getStatus(reg = reg)
-outpaths <- subsetWF(args, slot = "output", subset = 1, index = 1)
-file.exists(outpaths)
-sapply(1:length(outpaths), function(x) loadResult(reg, id = x)) # Works after job completion
-Generate a table of read and alignment counts for all samples.
-read_statsDF <- alignStats(args)
-write.table(read_statsDF, "results/alignStats.xls", row.names = FALSE, quote = FALSE,
- sep = "\t")
-The following shows the first four lines of the sample alignment stats file
-provided by the systemPipeR
package. For simplicity the number of PE reads
-is multiplied here by 2 to approximate proper alignment frequencies where each
-read in a pair is counted.
read.table(system.file("extdata", "alignStats.xls", package = "systemPipeR"), header = TRUE)[1:4,
- ]
-## FileName Nreads2x Nalign Perc_Aligned Nalign_Primary Perc_Aligned_Primary
-## 1 M1A 192918 177961 92.24697 177961 92.24697
-## 2 M1B 197484 159378 80.70426 159378 80.70426
-## 3 A1A 189870 176055 92.72397 176055 92.72397
-## 4 A1B 188854 147768 78.24457 147768 78.24457
-Parallelization of read/alignment stats on single machine with multiple cores.
-f <- function(x) alignStats(args[x])
-read_statsList <- bplapply(seq(along = args), f, BPPARAM = MulticoreParam(workers = 8))
-read_statsDF <- do.call("rbind", read_statsList)
-Parallelization of read/alignment stats via scheduler (e.g. Slurm) across several compute nodes.
-library(BiocParallel)
-library(batchtools)
-f <- function(x) {
- library(systemPipeR)
- targets <- system.file("extdata", "targets.txt", package = "systemPipeR")
- dir_path <- "param/cwl/hisat2/hisat2-se" ## TODO: replace path to system.file
- args <- loadWorkflow(targets = targets, wf_file = "hisat2-mapping-se.cwl", input_file = "hisat2-mapping-se.yml",
- dir_path = dir_path)
- args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
- args <- output_update(args, dir = FALSE, replace = TRUE, extension = c(".sam",
- ".bam"))
- alignStats(args[x])
-}
-resources <- list(walltime = 120, ntasks = 1, ncpus = 4, memory = 1024)
-param <- BatchtoolsParam(workers = 4, cluster = "slurm", template = "batchtools.slurm.tmpl",
- resources = resources)
-read_statsList <- bplapply(seq(along = args), f, BPPARAM = param)
-read_statsDF <- do.call("rbind", read_statsList)
-Download miRNA genes from miRBase.
-system("wget ftp://mirbase.org/pub/mirbase/19/genomes/My_species.gff3 -P ./data/")
-gff <- import.gff("./data/My_species.gff3")
-gff <- split(gff, elementMetadata(gff)$ID)
-bams <- names(bampaths)
-names(bams) <- targets$SampleName
-bfl <- BamFileList(bams, yieldSize = 50000, index = character())
-countDFmiR <- summarizeOverlaps(gff, bfl, mode = "Union", ignore.strand = FALSE,
- inter.feature = FALSE) # Note: inter.feature=FALSE important since pre and mature miRNA ranges overlap
-rpkmDFmiR <- apply(countDFmiR, 2, function(x) returnRPKM(counts = x, gffsub = gff))
-write.table(assays(countDFmiR)$counts, "results/countDFmiR.xls", col.names = NA,
- quote = FALSE, sep = "\t")
-write.table(rpkmDFmiR, "results/rpkmDFmiR.xls", col.names = NA, quote = FALSE, sep = "\t")
-The following computes the sample-wise Spearman correlation coefficients from the rlog
(regularized-logarithm) transformed expression values generated with the DESeq2
package. After transformation to a distance matrix, hierarchical clustering is performed with the hclust
function and the result is plotted as a dendrogram (sample_tree.pdf).
library(DESeq2, warn.conflicts = FALSE, quietly = TRUE)
-library(ape, warn.conflicts = FALSE)
-countDFpath <- system.file("extdata", "countDFeByg.xls", package = "systemPipeR")
-countDF <- as.matrix(read.table(countDFpath))
-colData <- data.frame(row.names = targets.as.df(targets(args))$SampleName, condition = targets.as.df(targets(args))$Factor)
-dds <- DESeqDataSetFromMatrix(countData = countDF, colData = colData, design = ~condition)
-## Warning in DESeqDataSet(se, design = design, ignoreRank): some variables in
-## design formula are characters, converting to factors
-d <- cor(assay(rlog(dds)), method = "spearman")
-hc <- hclust(dist(1 - d))
-plot.phylo(as.phylo(hc), type = "p", edge.col = 4, edge.width = 3, show.node.label = TRUE,
- no.margin = TRUE)
-
-rlog
values.
-Alternatively, the clustering can be performed with RPKM
normalized expression values. In combination with Spearman correlation the results of the two clustering methods are often relatively similar.
rpkmDFeBygpath <- system.file("extdata", "rpkmDFeByg.xls", package = "systemPipeR")
-rpkmDFeByg <- read.table(rpkmDFeBygpath, check.names = FALSE)
-rpkmDFeByg <- rpkmDFeByg[rowMeans(rpkmDFeByg) > 50, ]
-d <- cor(rpkmDFeByg, method = "spearman")
-hc <- hclust(as.dist(1 - d))
-plot.phylo(as.phylo(hc), type = "p", edge.col = "blue", edge.width = 2, show.node.label = TRUE,
- no.margin = TRUE)
-edgeR
The following run_edgeR
function is a convenience wrapper for
-identifying differentially expressed genes (DEGs) in batch mode with
-edgeR
’s GML method (Robinson, McCarthy, and Smyth 2010) for any number of
-pairwise sample comparisons specified under the cmp
argument. Users
-are strongly encouraged to consult the
-edgeR
vignette
-for more detailed information on this topic and how to properly run edgeR
-on data sets with more complex experimental designs.
targetspath <- system.file("extdata", "targets.txt", package = "systemPipeR")
-targets <- read.delim(targetspath, comment = "#")
-cmp <- readComp(file = targetspath, format = "matrix", delim = "-")
-cmp[[1]]
-## [,1] [,2]
-## [1,] "M1" "A1"
-## [2,] "M1" "V1"
-## [3,] "A1" "V1"
-## [4,] "M6" "A6"
-## [5,] "M6" "V6"
-## [6,] "A6" "V6"
-## [7,] "M12" "A12"
-## [8,] "M12" "V12"
-## [9,] "A12" "V12"
-countDFeBygpath <- system.file("extdata", "countDFeByg.xls", package = "systemPipeR")
-countDFeByg <- read.delim(countDFeBygpath, row.names = 1)
-edgeDF <- run_edgeR(countDF = countDFeByg, targets = targets, cmp = cmp[[1]], independent = FALSE,
- mdsplot = "")
-## Disp = 0.21829 , BCV = 0.4672
-Filter and plot DEG results for up and down-regulated genes. Because of the small size of the toy data set used by this vignette, the FDR value has been set to a relatively high threshold (here 10%). More commonly used FDR cutoffs are 1% or 5%. The definition of ‘up’ and ‘down’ is given in the corresponding help file. To open it, type ?filterDEGs
in the R console.
DEG_list <- filterDEGs(degDF = edgeDF, filter = c(Fold = 2, FDR = 10))
-
-edgeR
.
-names(DEG_list)
-## [1] "UporDown" "Up" "Down" "Summary"
-DEG_list$Summary[1:4, ]
-## Comparisons Counts_Up_or_Down Counts_Up Counts_Down
-## M1-A1 M1-A1 0 0 0
-## M1-V1 M1-V1 1 1 0
-## A1-V1 A1-V1 1 1 0
-## M6-A6 M6-A6 0 0 0
-DESeq2
The following run_DESeq2
function is a convenience wrapper for
-identifying DEGs in batch mode with DESeq2
(Love, Huber, and Anders 2014) for any number of
-pairwise sample comparisons specified under the cmp
argument. Users
-are strongly encouraged to consult the
-DESeq2
vignette
-for more detailed information on this topic and how to properly run DESeq2
-on data sets with more complex experimental designs.
degseqDF <- run_DESeq2(countDF = countDFeByg, targets = targets, cmp = cmp[[1]],
- independent = FALSE)
-## Warning in DESeqDataSet(se, design = design, ignoreRank): some variables in
-## design formula are characters, converting to factors
-Filter and plot DEG results for up and down-regulated genes.
-DEG_list2 <- filterDEGs(degDF = degseqDF, filter = c(Fold = 2, FDR = 10))
-
-DESeq2
.
-The function overLapper
can compute Venn intersects for large numbers of sample sets (up to 20 or more) and vennPlot
can plot 2-5 way Venn diagrams. A useful feature is the possibility to combine the counts from several Venn comparisons with the same number of sample sets in a single Venn diagram (here for 4 up and down DEG sets).
vennsetup <- overLapper(DEG_list$Up[6:9], type = "vennsets")
-vennsetdown <- overLapper(DEG_list$Down[6:9], type = "vennsets")
-vennPlot(list(vennsetup, vennsetdown), mymain = "", mysub = "", colmode = 2, ccol = c("blue",
- "red"))
-
-The following shows how to obtain gene-to-GO mappings from biomaRt
(here for A. thaliana) and how to organize them for the downstream GO term enrichment analysis. Alternatively, the gene-to-GO mappings can be obtained for many organisms from Bioconductor’s *.db
genome annotation packages or GO annotation files provided by various genome databases. For each annotation, this relatively slow preprocessing step needs to be performed only once. Subsequently, the preprocessed data can be loaded with the load
function as shown in the next subsection.
library("biomaRt")
-listMarts() # To choose BioMart database
-listMarts(host = "plants.ensembl.org")
-m <- useMart("plants_mart", host = "plants.ensembl.org")
-listDatasets(m)
-m <- useMart("plants_mart", dataset = "athaliana_eg_gene", host = "plants.ensembl.org")
-listAttributes(m) # Choose data types you want to download
-go <- getBM(attributes = c("go_id", "tair_locus", "namespace_1003"), mart = m)
-go <- go[go[, 3] != "", ]
-go[, 3] <- as.character(go[, 3])
-go[go[, 3] == "molecular_function", 3] <- "F"
-go[go[, 3] == "biological_process", 3] <- "P"
-go[go[, 3] == "cellular_component", 3] <- "C"
-go[1:4, ]
-dir.create("./data/GO")
-write.table(go, "data/GO/GOannotationsBiomart_mod.txt", quote = FALSE, row.names = FALSE,
- col.names = FALSE, sep = "\t")
-catdb <- makeCATdb(myfile = "data/GO/GOannotationsBiomart_mod.txt", lib = NULL, org = "",
- colno = c(1, 2, 3), idconv = NULL)
-save(catdb, file = "data/GO/catdb.RData")
-Apply the enrichment analysis to the DEG sets obtained in the above differential expression analysis. Note, in the following example the FDR filter is set here to an unreasonably high value, simply because of the small size of the toy data set used in this vignette. Batch enrichment analysis of many gene sets is performed with the GOCluster_Report
function. When method="all"
, it returns all GO terms passing the p-value cutoff specified under the cutoff
arguments. When method="slim"
, it returns only the GO terms specified under the myslimv
argument. The given example shows how one can obtain such a GO slim vector from BioMart for a specific organism.
load("data/GO/catdb.RData")
-DEG_list <- filterDEGs(degDF = edgeDF, filter = c(Fold = 2, FDR = 50), plot = FALSE)
-up_down <- DEG_list$UporDown
-names(up_down) <- paste(names(up_down), "_up_down", sep = "")
-up <- DEG_list$Up
-names(up) <- paste(names(up), "_up", sep = "")
-down <- DEG_list$Down
-names(down) <- paste(names(down), "_down", sep = "")
-DEGlist <- c(up_down, up, down)
-DEGlist <- DEGlist[sapply(DEGlist, length) > 0]
-BatchResult <- GOCluster_Report(catdb = catdb, setlist = DEGlist, method = "all",
- id_type = "gene", CLSZ = 2, cutoff = 0.9, gocats = c("MF", "BP", "CC"), recordSpecGO = NULL)
-library("biomaRt")
-m <- useMart("plants_mart", dataset = "athaliana_eg_gene", host = "plants.ensembl.org")
-goslimvec <- as.character(getBM(attributes = c("goslim_goa_accession"), mart = m)[,
- 1])
-BatchResultslim <- GOCluster_Report(catdb = catdb, setlist = DEGlist, method = "slim",
- id_type = "gene", myslimv = goslimvec, CLSZ = 10, cutoff = 0.01, gocats = c("MF",
- "BP", "CC"), recordSpecGO = NULL)
-The data.frame
generated by GOCluster_Report
can be plotted with the goBarplot
function. Because of the variable size of the sample sets, it may not always be desirable to show the results from different DEG sets in the same bar plot. Plotting single sample sets is achieved by subsetting the input data frame as shown in the first line of the following example.
gos <- BatchResultslim[grep("M6-V6_up_down", BatchResultslim$CLID), ]
-gos <- BatchResultslim
-pdf("GOslimbarplotMF.pdf", height = 8, width = 10)
-goBarplot(gos, gocat = "MF")
-dev.off()
-goBarplot(gos, gocat = "BP")
-goBarplot(gos, gocat = "CC")
-
-The following example performs hierarchical clustering on the rlog
transformed expression matrix subsetted by the DEGs identified in the
-above differential expression analysis. It uses a Pearson correlation-based distance measure and complete linkage for cluster join.
library(pheatmap)
-geneids <- unique(as.character(unlist(DEG_list[[1]])))
-y <- assay(rlog(dds))[geneids, ]
-pdf("heatmap1.pdf")
-pheatmap(y, scale = "row", clustering_distance_rows = "correlation", clustering_distance_cols = "correlation")
-dev.off()
-