updateExamples

urmi-21 · Feb 19, 2020 · c047611 · c047611
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diff --git a/.gitignore b/.gitignore
@@ -6,12 +6,12 @@
 #ignore files generated by test
 tests/testout
 #ignore files generated by examples
-examples/Athaliana_transcript_assembly/athal_out
-examples/Maize_lncRNA_prediction/maize_out
-examples/Human_annotation_snakemake/out
-examples/Human_annotation_snakemake/human_data
-examples/Human_annotation_snakemake/hisat_index
-examples/Human_annotation_snakemake/.snakemake
+examples(case-studies)/Athaliana_transcript_assembly/athal_out
+examples(case-studies)/Maize_lncRNA_prediction/maize_out
+examples(case-studies)/Human_annotation_snakemake/out
+examples(case-studies)/Human_annotation_snakemake/human_data
+examples(case-studies)/Human_annotation_snakemake/hisat_index
+examples(case-studies)/Human_annotation_snakemake/.snakemake
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

diff --git a/..._assembly/2020-01-29-12_00_45_pyrpipe.pdf → ..._assembly/2020-01-29-12_00_45_pyrpipe.pdf b/..._assembly/2020-01-29-12_00_45_pyrpipe.pdf → ..._assembly/2020-01-29-12_00_45_pyrpipe.pdf
diff --git a/...t_assembly/2020-01-29-12_00_45_pyrpipe.sh → ...t_assembly/2020-01-29-12_00_45_pyrpipe.sh b/...t_assembly/2020-01-29-12_00_45_pyrpipe.sh → ...t_assembly/2020-01-29-12_00_45_pyrpipe.sh
diff --git a/...embly/Athaliana_transcript_assembly.ipynb → ...embly/Athaliana_transcript_assembly.ipynb b/...embly/Athaliana_transcript_assembly.ipynb → ...embly/Athaliana_transcript_assembly.ipynb
diff --git a/...s/Athaliana_transcript_assembly/README.md → ...)/Athaliana_transcript_assembly/README.md b/...s/Athaliana_transcript_assembly/README.md → ...)/Athaliana_transcript_assembly/README.md
diff --git a/...thaliana_transcript_assembly/adapters2.fa → ...thaliana_transcript_assembly/adapters2.fa b/...thaliana_transcript_assembly/adapters2.fa → ...thaliana_transcript_assembly/adapters2.fa
diff --git a/...ly/benchmark_reports/program_box_data.csv → ...ly/benchmark_reports/program_box_data.csv b/...ly/benchmark_reports/program_box_data.csv → ...ly/benchmark_reports/program_box_data.csv
diff --git a/...ly/benchmark_reports/program_boxplots.png → ...ly/benchmark_reports/program_boxplots.png b/...ly/benchmark_reports/program_boxplots.png → ...ly/benchmark_reports/program_boxplots.png
diff --git a/...bly/benchmark_reports/program_summary.png → ...bly/benchmark_reports/program_summary.png b/...bly/benchmark_reports/program_summary.png → ...bly/benchmark_reports/program_summary.png
diff --git a/...bly/benchmark_reports/time_per_object.csv → ...bly/benchmark_reports/time_per_object.csv b/...bly/benchmark_reports/time_per_object.csv → ...bly/benchmark_reports/time_per_object.csv
diff --git a/...bly/benchmark_reports/time_per_object.png → ...bly/benchmark_reports/time_per_object.png b/...bly/benchmark_reports/time_per_object.png → ...bly/benchmark_reports/time_per_object.png
diff --git a/...ly/benchmark_reports/time_per_program.csv → ...ly/benchmark_reports/time_per_program.csv b/...ly/benchmark_reports/time_per_program.csv → ...ly/benchmark_reports/time_per_program.csv
diff --git a/...ly/benchmark_reports/time_per_program.png → ...ly/benchmark_reports/time_per_program.png b/...ly/benchmark_reports/time_per_program.png → ...ly/benchmark_reports/time_per_program.png
diff --git a/...liana_transcript_assembly/environment.yml → ...liana_transcript_assembly/environment.yml b/...liana_transcript_assembly/environment.yml → ...liana_transcript_assembly/environment.yml
diff --git a/...assembly/multiqc_data/multiqc_bowtie2.txt → ...assembly/multiqc_data/multiqc_bowtie2.txt b/...assembly/multiqc_data/multiqc_bowtie2.txt → ...assembly/multiqc_data/multiqc_bowtie2.txt
diff --git a/...t_assembly/multiqc_data/multiqc_data.json → ...t_assembly/multiqc_data/multiqc_data.json b/...t_assembly/multiqc_data/multiqc_data.json → ...t_assembly/multiqc_data/multiqc_data.json
diff --git a/...ly/multiqc_data/multiqc_general_stats.txt → ...ly/multiqc_data/multiqc_general_stats.txt b/...ly/multiqc_data/multiqc_general_stats.txt → ...ly/multiqc_data/multiqc_general_stats.txt
diff --git a/...multiqc_qualimap_bamqc_genome_results.txt → ...multiqc_qualimap_bamqc_genome_results.txt b/...multiqc_qualimap_bamqc_genome_results.txt → ...multiqc_qualimap_bamqc_genome_results.txt
diff --git a/...assembly/multiqc_data/multiqc_sources.txt → ...assembly/multiqc_data/multiqc_sources.txt b/...assembly/multiqc_data/multiqc_sources.txt → ...assembly/multiqc_data/multiqc_sources.txt
diff --git a/...a_transcript_assembly/multiqc_report.html → ...a_transcript_assembly/multiqc_report.html b/...a_transcript_assembly/multiqc_report.html → ...a_transcript_assembly/multiqc_report.html
diff --git a/...ples/Human_annotation_snakemake/README.md → ...ies)/Human_annotation_snakemake/README.md b/...ples/Human_annotation_snakemake/README.md → ...ies)/Human_annotation_snakemake/README.md
diff --git a/...les/Human_annotation_snakemake/SRRids.txt → ...es)/Human_annotation_snakemake/SRRids.txt b/...les/Human_annotation_snakemake/SRRids.txt → ...es)/Human_annotation_snakemake/SRRids.txt
diff --git a/...ples/Human_annotation_snakemake/Snakefile → ...ies)/Human_annotation_snakemake/Snakefile b/...ples/Human_annotation_snakemake/Snakefile → ...ies)/Human_annotation_snakemake/Snakefile
diff --git a/...es/Human_annotation_snakemake/adapters.fa → ...s)/Human_annotation_snakemake/adapters.fa b/...es/Human_annotation_snakemake/adapters.fa → ...s)/Human_annotation_snakemake/adapters.fa
diff --git a/...s/Human_annotation_snakemake/build_env.sh → ...)/Human_annotation_snakemake/build_env.sh b/...s/Human_annotation_snakemake/build_env.sh → ...)/Human_annotation_snakemake/build_env.sh
diff --git a/.../Human_annotation_snakemake/conda_env.yml → .../Human_annotation_snakemake/conda_env.yml b/.../Human_annotation_snakemake/conda_env.yml → .../Human_annotation_snakemake/conda_env.yml
diff --git a/...es/Human_annotation_snakemake/config.yaml → ...s)/Human_annotation_snakemake/config.yaml b/...es/Human_annotation_snakemake/config.yaml → ...s)/Human_annotation_snakemake/config.yaml
diff --git a/examples/Human_annotation_snakemake/dag.svg → ...udies)/Human_annotation_snakemake/dag.svg b/examples/Human_annotation_snakemake/dag.svg → ...udies)/Human_annotation_snakemake/dag.svg
diff --git a/...es/Human_annotation_snakemake/params.yaml → ...s)/Human_annotation_snakemake/params.yaml b/...es/Human_annotation_snakemake/params.yaml → ...s)/Human_annotation_snakemake/params.yaml
diff --git a/examples/Integrating third-party tools.ipynb → ...dies)/Integrating third-party tools.ipynb b/examples/Integrating third-party tools.ipynb → ...dies)/Integrating third-party tools.ipynb
diff --git a/...rediction/2020-01-22-18_14_47_pyrpipe.pdf → ...rediction/2020-01-22-18_14_47_pyrpipe.pdf b/...rediction/2020-01-22-18_14_47_pyrpipe.pdf → ...rediction/2020-01-22-18_14_47_pyrpipe.pdf
diff --git a/...prediction/2020-01-22-18_14_47_pyrpipe.sh → ...prediction/2020-01-22-18_14_47_pyrpipe.sh b/...prediction/2020-01-22-18_14_47_pyrpipe.sh → ...prediction/2020-01-22-18_14_47_pyrpipe.sh
diff --git a/...ize_lncRNA_prediction/Maize_lncRNAs.ipynb → ...ize_lncRNA_prediction/Maize_lncRNAs.ipynb b/...ize_lncRNA_prediction/Maize_lncRNAs.ipynb → ...ize_lncRNA_prediction/Maize_lncRNAs.ipynb
diff --git a/examples/Maize_lncRNA_prediction/README.md → ...tudies)/Maize_lncRNA_prediction/README.md b/examples/Maize_lncRNA_prediction/README.md → ...tudies)/Maize_lncRNA_prediction/README.md
diff --git a/...on/benchmark_reports/program_box_data.csv → ...on/benchmark_reports/program_box_data.csv b/...on/benchmark_reports/program_box_data.csv → ...on/benchmark_reports/program_box_data.csv
diff --git a/...on/benchmark_reports/program_boxplots.png → ...on/benchmark_reports/program_boxplots.png b/...on/benchmark_reports/program_boxplots.png → ...on/benchmark_reports/program_boxplots.png
diff --git a/...ion/benchmark_reports/program_summary.png → ...ion/benchmark_reports/program_summary.png b/...ion/benchmark_reports/program_summary.png → ...ion/benchmark_reports/program_summary.png
diff --git a/...ion/benchmark_reports/time_per_object.csv → ...ion/benchmark_reports/time_per_object.csv b/...ion/benchmark_reports/time_per_object.csv → ...ion/benchmark_reports/time_per_object.csv
diff --git a/...ion/benchmark_reports/time_per_object.png → ...ion/benchmark_reports/time_per_object.png b/...ion/benchmark_reports/time_per_object.png → ...ion/benchmark_reports/time_per_object.png
diff --git a/...on/benchmark_reports/time_per_program.csv → ...on/benchmark_reports/time_per_program.csv b/...on/benchmark_reports/time_per_program.csv → ...on/benchmark_reports/time_per_program.csv
diff --git a/...on/benchmark_reports/time_per_program.png → ...on/benchmark_reports/time_per_program.png b/...on/benchmark_reports/time_per_program.png → ...on/benchmark_reports/time_per_program.png
diff --git a/...s/Maize_lncRNA_prediction/environment.yml → ...)/Maize_lncRNA_prediction/environment.yml b/...s/Maize_lncRNA_prediction/environment.yml → ...)/Maize_lncRNA_prediction/environment.yml
diff --git a/..._report/multiqc_data/multiqc_cutadapt.txt → ..._report/multiqc_data/multiqc_cutadapt.txt b/..._report/multiqc_data/multiqc_cutadapt.txt → ..._report/multiqc_data/multiqc_cutadapt.txt
diff --git a/...iqc_report/multiqc_data/multiqc_data.json → ...iqc_report/multiqc_data/multiqc_data.json b/...iqc_report/multiqc_data/multiqc_data.json → ...iqc_report/multiqc_data/multiqc_data.json
diff --git a/...rt/multiqc_data/multiqc_general_stats.txt → ...rt/multiqc_data/multiqc_general_stats.txt b/...rt/multiqc_data/multiqc_general_stats.txt → ...rt/multiqc_data/multiqc_general_stats.txt
diff --git a/...multiqc_qualimap_bamqc_genome_results.txt → ...multiqc_qualimap_bamqc_genome_results.txt b/...multiqc_qualimap_bamqc_genome_results.txt → ...multiqc_qualimap_bamqc_genome_results.txt
diff --git a/...c_report/multiqc_data/multiqc_sources.txt → ...c_report/multiqc_data/multiqc_sources.txt b/...c_report/multiqc_data/multiqc_sources.txt → ...c_report/multiqc_data/multiqc_sources.txt
diff --git a/...iction/multiqc_report/multiqc_report.html → ...iction/multiqc_report/multiqc_report.html b/...iction/multiqc_report/multiqc_report.html → ...iction/multiqc_report/multiqc_report.html
diff --git a/...lncRNA_prediction/tmp/SRR3098744_STAR.txt → ...lncRNA_prediction/tmp/SRR3098744_STAR.txt b/...lncRNA_prediction/tmp/SRR3098744_STAR.txt → ...lncRNA_prediction/tmp/SRR3098744_STAR.txt
diff --git a/...rediction/tmp/SRR3098744_fasterq-dump.txt → ...rediction/tmp/SRR3098744_fasterq-dump.txt b/...rediction/tmp/SRR3098744_fasterq-dump.txt → ...rediction/tmp/SRR3098744_fasterq-dump.txt
diff --git a/...RNA_prediction/tmp/SRR3098744_gffread.txt → ...RNA_prediction/tmp/SRR3098744_gffread.txt b/...RNA_prediction/tmp/SRR3098744_gffread.txt → ...RNA_prediction/tmp/SRR3098744_gffread.txt
diff --git a/...iction/tmp/SRR3098744_plncpro predict.txt → ...iction/tmp/SRR3098744_plncpro predict.txt b/...iction/tmp/SRR3098744_plncpro predict.txt → ...iction/tmp/SRR3098744_plncpro predict.txt
diff --git a/...NA_prediction/tmp/SRR3098744_prefetch.txt → ...NA_prediction/tmp/SRR3098744_prefetch.txt b/...NA_prediction/tmp/SRR3098744_prefetch.txt → ...NA_prediction/tmp/SRR3098744_prefetch.txt
diff --git a/...A_prediction/tmp/SRR3098744_stringtie.txt → ...A_prediction/tmp/SRR3098744_stringtie.txt b/...A_prediction/tmp/SRR3098744_stringtie.txt → ...A_prediction/tmp/SRR3098744_stringtie.txt
diff --git a/...prediction/tmp/SRR3098744_trim_galore.txt → ...prediction/tmp/SRR3098744_trim_galore.txt b/...prediction/tmp/SRR3098744_trim_galore.txt → ...prediction/tmp/SRR3098744_trim_galore.txt
diff --git a/...NA_prediction/tmp/SRR3098745_prefetch.txt → ...NA_prediction/tmp/SRR3098745_prefetch.txt b/...NA_prediction/tmp/SRR3098745_prefetch.txt → ...NA_prediction/tmp/SRR3098745_prefetch.txt
diff --git a/...lncRNA_prediction/tmp/SRR3098746_STAR.txt → ...lncRNA_prediction/tmp/SRR3098746_STAR.txt b/...lncRNA_prediction/tmp/SRR3098746_STAR.txt → ...lncRNA_prediction/tmp/SRR3098746_STAR.txt
diff --git a/...rediction/tmp/SRR3098746_fasterq-dump.txt → ...rediction/tmp/SRR3098746_fasterq-dump.txt b/...rediction/tmp/SRR3098746_fasterq-dump.txt → ...rediction/tmp/SRR3098746_fasterq-dump.txt
diff --git a/...RNA_prediction/tmp/SRR3098746_gffread.txt → ...RNA_prediction/tmp/SRR3098746_gffread.txt b/...RNA_prediction/tmp/SRR3098746_gffread.txt → ...RNA_prediction/tmp/SRR3098746_gffread.txt
diff --git a/...iction/tmp/SRR3098746_plncpro predict.txt → ...iction/tmp/SRR3098746_plncpro predict.txt b/...iction/tmp/SRR3098746_plncpro predict.txt → ...iction/tmp/SRR3098746_plncpro predict.txt
diff --git a/...NA_prediction/tmp/SRR3098746_prefetch.txt → ...NA_prediction/tmp/SRR3098746_prefetch.txt b/...NA_prediction/tmp/SRR3098746_prefetch.txt → ...NA_prediction/tmp/SRR3098746_prefetch.txt
diff --git a/...A_prediction/tmp/SRR3098746_stringtie.txt → ...A_prediction/tmp/SRR3098746_stringtie.txt b/...A_prediction/tmp/SRR3098746_stringtie.txt → ...A_prediction/tmp/SRR3098746_stringtie.txt
diff --git a/...prediction/tmp/SRR3098746_trim_galore.txt → ...prediction/tmp/SRR3098746_trim_galore.txt b/...prediction/tmp/SRR3098746_trim_galore.txt → ...prediction/tmp/SRR3098746_trim_galore.txt
diff --git a/examples/sample_data/blast_out → examples(case-studies)/sample_data/blast_out b/examples/sample_data/blast_out → examples(case-studies)/sample_data/blast_out
diff --git a/examples/sample_data/blast_out2 → ...ples(case-studies)/sample_data/blast_out2 b/examples/sample_data/blast_out2 → ...ples(case-studies)/sample_data/blast_out2
diff --git a/examples/sample_data/pldb/dbcmd → ...ples(case-studies)/sample_data/pldb/dbcmd b/examples/sample_data/pldb/dbcmd → ...ples(case-studies)/sample_data/pldb/dbcmd
diff --git a/examples/sample_data/pldb/mydb.phr → ...s(case-studies)/sample_data/pldb/mydb.phr b/examples/sample_data/pldb/mydb.phr → ...s(case-studies)/sample_data/pldb/mydb.phr
diff --git a/examples/sample_data/pldb/mydb.pin → ...s(case-studies)/sample_data/pldb/mydb.pin b/examples/sample_data/pldb/mydb.pin → ...s(case-studies)/sample_data/pldb/mydb.pin
diff --git a/examples/sample_data/pldb/mydb.psq → ...s(case-studies)/sample_data/pldb/mydb.psq b/examples/sample_data/pldb/mydb.psq → ...s(case-studies)/sample_data/pldb/mydb.psq
diff --git a/examples/sample_data/pldb/un.fasta → ...s(case-studies)/sample_data/pldb/un.fasta b/examples/sample_data/pldb/un.fasta → ...s(case-studies)/sample_data/pldb/un.fasta
diff --git a/examples/sample_data/test.fa → examples(case-studies)/sample_data/test.fa b/examples/sample_data/test.fa → examples(case-studies)/sample_data/test.fa
diff --git a/examples/Maize_lncRNA_prediction/pyrpipe_logs/2020-01-22-18_14_47_pyrpipe.log b/examples/Maize_lncRNA_prediction/pyrpipe_logs/2020-01-22-18_14_47_pyrpipe.log
diff --git a/examples/Maize_lncRNA_prediction/pyrpipe_logs/2020-01-22-18_14_47_pyrpipeENV.log b/examples/Maize_lncRNA_prediction/pyrpipe_logs/2020-01-22-18_14_47_pyrpipeENV.log