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Update to pypeflow-2.0.0
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Christopher Dunn committed Mar 26, 2018
1 parent dc037eb commit bbd019e
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8 changes: 4 additions & 4 deletions .gitmodules
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Expand Up @@ -24,21 +24,21 @@
branch = develop
[submodule "FALCON_unzip"]
path = FALCON_unzip
url = git://github.com/PacificBiosciences/FALCON_unzip
url = https://github.com/PacificBiosciences/FALCON_unzip
branch = master
[submodule "FALCON-make"]
path = FALCON-make
url = git://github.com/pb-cdunn/FALCON-make.git
url = https://github.com/pb-cdunn/FALCON-make.git
branch = master
[submodule "FALCON-examples"]
path = FALCON-examples
url = git://github.com/pb-cdunn/FALCON-examples.git
url = https://github.com/pb-cdunn/FALCON-examples.git
branch = master
[submodule "git-sym"]
path = git-sym
url = https://cdunn2001@github.com/cdunn2001/git-sym.git
branch = master
[submodule "nim-falcon"]
path = nim-falcon
url = git://github.com/bio-nim/nim-falcon
url = https://github.com/bio-nim/nim-falcon
branch = dev
2 changes: 1 addition & 1 deletion FALCON
Submodule FALCON updated 97 files
+1 −0 .gitignore
+1 −0 bamboo_build.sh
+4 −4 falcon_kit/FastaReader.py
+1 −1 falcon_kit/__init__.py
+1 −1 falcon_kit/bash.py
+1 −1 falcon_kit/falcon_kit.py
+1 −1 falcon_kit/fc_asm_graph.py
+3 −3 falcon_kit/functional.py
+2 −2 falcon_kit/gfa_graph.py
+7 −1 falcon_kit/io.py
+1 −1 falcon_kit/mains/LAmerge.py
+1 −1 falcon_kit/mains/LAsort.py
+1 −1 falcon_kit/mains/actg_coordinate.py
+1 −1 falcon_kit/mains/build_pdb.py
+1 −1 falcon_kit/mains/build_rdb.py
+2 −2 falcon_kit/mains/calc_cutoff.py
+1 −1 falcon_kit/mains/consensus.py
+1 −1 falcon_kit/mains/consensus_gather_fasta_fofn.py
+1 −1 falcon_kit/mains/consensus_scatter.py
+1 −1 falcon_kit/mains/consensus_split.py
+1 −1 falcon_kit/mains/consensus_task.py
+1 −1 falcon_kit/mains/contig_annotate.py
+1 −1 falcon_kit/mains/copy_fofn.py
+2 −2 falcon_kit/mains/copy_mapped.py
+1 −1 falcon_kit/mains/ctg_link_analysis.py
+1 −1 falcon_kit/mains/daligner.py
+1 −1 falcon_kit/mains/daligner_gather_las_list.py
+1 −1 falcon_kit/mains/daligner_scatter.py
+1 −1 falcon_kit/mains/daligner_split.py
+1 −1 falcon_kit/mains/dedup_a_tigs.py
+1 −1 falcon_kit/mains/fasta2fasta.py
+1 −1 falcon_kit/mains/fetch_reads.py
+1 −1 falcon_kit/mains/gen_gfa_v1.py
+1 −1 falcon_kit/mains/generate_read_to_ctg_map.py
+1 −1 falcon_kit/mains/generic_gather.py
+1 −1 falcon_kit/mains/generic_run_units_of_work.py
+1 −1 falcon_kit/mains/generic_scatter_one_uow.py
+1 −1 falcon_kit/mains/generic_unsplit.py
+1 −1 falcon_kit/mains/get_read_ctg_map.py
+1 −1 falcon_kit/mains/graph_to_contig.py
+1 −1 falcon_kit/mains/graph_to_utgs.py
+1 −1 falcon_kit/mains/hgap4_adapt.py
+1 −1 falcon_kit/mains/las_merge.py
+1 −1 falcon_kit/mains/las_merge_gather.py
+1 −1 falcon_kit/mains/las_merge_scatter.py
+1 −1 falcon_kit/mains/las_merge_split.py
+1 −1 falcon_kit/mains/ovlp_filter.py
+2 −2 falcon_kit/mains/ovlp_stats.py
+1 −1 falcon_kit/mains/ovlp_to_graph.py
+1 −1 falcon_kit/mains/pr_ctg_track.py
+1 −1 falcon_kit/mains/report_pre_assembly.py
+1 −1 falcon_kit/mains/rr_ctg_track.py
+26 −45 falcon_kit/mains/run1.py
+2 −2 falcon_kit/mains/symlink_mapped.py
+1 −1 falcon_kit/mains/task_report_pre_assembly.py
+1 −1 falcon_kit/mains/tasks.py
+1 −1 falcon_kit/multiproc.py
+9 −3 falcon_kit/pype.py
+1 −1 falcon_kit/pype_tasks.py
+154 −100 falcon_kit/run_support.py
+2 −2 falcon_kit/snakemake.py
+1 −1 falcon_kit/stats_preassembly.py
+9 −6 falcon_kit/util/io.py
+1 −1 falcon_kit/util/system.py
+1 −1 setup.py
+1 −1 src/py_scripts/fc_actg_coordinate.py
+1 −1 src/py_scripts/fc_consensus.py
+1 −1 src/py_scripts/fc_contig_annotate.py
+1 −1 src/py_scripts/fc_ctg_link_analysis.py
+1 −1 src/py_scripts/fc_dedup_a_tigs.py
+1 −1 src/py_scripts/fc_graph_to_contig.py
+1 −1 src/py_scripts/fc_graph_to_utgs.py
+1 −1 src/py_scripts/fc_ovlp_filter.py
+1 −1 src/py_scripts/fc_ovlp_stats.py
+1 −1 src/py_scripts/fc_ovlp_to_graph.py
+1 −1 src/py_scripts/fc_run.py
+1 −1 src/utils/fetch_preads.py
+5 −4 test/helpers.py
+1 −1 test/test_actg_coordinate.py
+2 −2 test/test_calc_cutoff.py
+1 −1 test/test_consensus.py
+1 −1 test/test_contig_annotate.py
+1 −1 test/test_ctg_link_analysis.py
+2 −2 test/test_functional.py
+2 −2 test/test_gen_gfa_v1.py
+4 −4 test/test_gfa_graph.py
+1 −1 test/test_graph_to_contig.py
+1 −1 test/test_graph_to_utgs.py
+1 −1 test/test_ovlp_filter.py
+1 −1 test/test_ovlp_stats.py
+1 −1 test/test_ovlp_to_graph.py
+1 −1 test/test_run.py
+1 −1 test/test_run_LG.py
+160 −0 test/test_run_support.py
+1 −1 test/test_stats_preassembly.py
+2 −2 test/test_util_io.py
+2 −2 test/test_util_system.py
2 changes: 1 addition & 1 deletion nim-falcon
Submodule nim-falcon updated 1 files
+1 −1 repos/cligen
2 changes: 1 addition & 1 deletion pypeFLOW
Submodule pypeFLOW updated 11 files
+1 −0 .gitignore
+1 −0 bamboo_build.sh
+51 −26 pwatcher/blocking.py
+105 −193 pwatcher/fs_based.py
+5 −4 pwatcher/network_based.py
+1 −1 pypeflow/io.py
+1 −1 pypeflow/sample_tasks.py
+46 −41 pypeflow/simple_pwatcher_bridge.py
+13 −4 pypeflow/tasks.py
+1 −1 setup.py
+7 −12 test/test_integ.py

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