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Update: gstama/collapse (#1057)
* 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 📦 NEW: Add galgal6 chr30 test data * 📦 NEW: Add gd-tama module * 🐛 FIX (TEMP): Update singularity container address * 📦 NEW: Add bamtools module * 📦 NEW: Rewrite and rename module (gstama => gstama/collapse) * 👌 IMPROVE: ignore test data * 👌 IMPROVE: Remove junk files * 👌 IMPROVE: Update output * 👌 IMPROVE: Add channel for publishing tama's metadata outputs * 👌 IMPROVE: Update process label * 🐛 FIX: Use depot.galxyproject.org url for singularity * 👌 IMPROVE: autoselect running mode * 🐛 FIX: correct gstama collapse bash test * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update tama package and label * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Update test * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 📦 NEW: Add galgal6 chr30 test data * 📦 NEW: Add gd-tama module * 🐛 FIX (TEMP): Update singularity container address * 📦 NEW: Add bamtools module * 📦 NEW: Rewrite and rename module (gstama => gstama/collapse) * 👌 IMPROVE: ignore test data * 👌 IMPROVE: Update output * 👌 IMPROVE: Add channel for publishing tama's metadata outputs * 👌 IMPROVE: Update process label * 🐛 FIX: Use depot.galxyproject.org url for singularity * 👌 IMPROVE: autoselect running mode * 🐛 FIX: correct gstama collapse bash test * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update tama package and label * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Update test * 👌 IMPROVE: delete unnecessary files * 👌 IMPROVE: Update + clean - Remove unnecessary files - Update to new versions.yml file - Better output channels * 👌 IMPROVE: Update meta.yml and output channels * 👌 IMPROVE: Remove useless files * 👌 IMPROVE: Remove automatic MODE setup * 👌 IMPROVE: Applied @jfy133 code modification suggestions * Update modules/gstama/collapse/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * 🐛 FIX: Add missing fasta option in meta.yml * 🐛 FIX: Fix typo * 🐛 FIX: Update package version * Update main.nf * Update meta.yml * Update modules/gstama/collapse/meta.yml * Apply suggestions from code review * Update tests/modules/gstama/collapse/main.nf * Update main.nf * 👌 IMPROVE: Update to gs-tama 1.0.3 * Update modules/gstama/collapse/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
Sébastien Guizard
GitHub
parent
ec15d0f9fd
commit
001d5071c2
2 changed files with 8 additions and 5 deletions
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@ -11,11 +11,12 @@ process GSTAMA_COLLAPSE {
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mode: params.publish_dir_mode,
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gs-tama=1.0.2" : null)
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conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gs-tama:1.0.2--hdfd78af_0"
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container "https://depot.galaxyproject.org/singularity/gs-tama:1.0.3--hdfd78af_0"
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} else {
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} else {
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container "quay.io/biocontainers/gs-tama:1.0.2--hdfd78af_0"
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container "quay.io/biocontainers/gs-tama:1.0.3--hdfd78af_0"
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}
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}
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input:
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input:
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@ -23,7 +24,7 @@ process GSTAMA_COLLAPSE {
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path fasta
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path fasta
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output:
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output:
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tuple val(meta), path("*.bed") , emit: bed
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tuple val(meta), path("*_collapsed.bed") , emit: bed
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tuple val(meta), path("*_trans_read.bed") , emit: bed_trans_reads
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tuple val(meta), path("*_trans_read.bed") , emit: bed_trans_reads
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tuple val(meta), path("*_local_density_error.txt"), emit: local_density_error
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tuple val(meta), path("*_local_density_error.txt"), emit: local_density_error
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tuple val(meta), path("*_polya.txt") , emit: polya
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tuple val(meta), path("*_polya.txt") , emit: polya
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@ -4,7 +4,7 @@
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- gstama
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- gstama
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- gstama/collapse
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- gstama/collapse
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files:
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files:
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- path: output/gstama/test_tc.bed
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- path: output/gstama/test_tc_collapsed.bed
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md5sum: e5105198ed970a33ae0ecaa7bff421d9
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md5sum: e5105198ed970a33ae0ecaa7bff421d9
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- path: output/gstama/test_tc_local_density_error.txt
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- path: output/gstama/test_tc_local_density_error.txt
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md5sum: b917ac1f14eccd590b6881a686f324d5
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md5sum: b917ac1f14eccd590b6881a686f324d5
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@ -18,5 +18,7 @@
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md5sum: 0ca1a32f33ef05242d897d913802554b
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md5sum: 0ca1a32f33ef05242d897d913802554b
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- path: output/gstama/test_tc_trans_report.txt
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- path: output/gstama/test_tc_trans_report.txt
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md5sum: 33a86c15ca2acce36b2a5962f4c1adc4
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md5sum: 33a86c15ca2acce36b2a5962f4c1adc4
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- path: output/gstama/test_tc_varcov.txt
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md5sum: 587fd899ff658eb66b1770a35283bfcb
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- path: output/gstama/test_tc_variants.txt
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- path: output/gstama/test_tc_variants.txt
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md5sum: 5b1165e9f33faba4f7207013fc27257e
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md5sum: 5b1165e9f33faba4f7207013fc27257e
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