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https://github.com/MillironX/nf-core_modules.git
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Update isoseq3/cluster (#856)
* 📦 NEW: Add isoseq3/cluster module * 🐛FIX: Fix reports channel and add .pbi to it * 🐛FIX: Fix report channel definition * 👌IMPROVE: Move .pbi file into reports channel * 👌IMPROVE: remove --use_qvs option from command line * 👌 IMPROVE: Add in addParams removed options from command line * 👌 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 * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 📦 NEW: Add galgal6 chr30 test data * 📦 NEW: Add bamtools module * 👌 IMPROVE: Ignore test data * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: add singletons parameter and improve outputs * 🐛 FIX: Update test with last module model * 👌 IMPROVE: Add test tag * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update test data config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Remove unused index * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Fill contains args * 📦 NEW: Add isoseq3/cluster module * 🐛FIX: Fix reports channel and add .pbi to it * 🐛FIX: Fix report channel definition * 👌IMPROVE: Move .pbi file into reports channel * 👌IMPROVE: remove --use_qvs option from command line * 👌 IMPROVE: Add in addParams removed options from command line * 👌 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 * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: add singletons parameter and improve outputs * 🐛 FIX: Update test with last module model * 👌 IMPROVE: Add test tag * 👌 IMPROVE: Update test data config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Remove unused index * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Fill contains args * 👌 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 bamtools module * 👌 IMPROVE: Ignore test data * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Update code to new versions capture + better output channels * 👌 IMPROVE: Update with new versions.yml file * 🐛 FIX: Update meta.yml + correct typos * 👌 IMPROVE: Clean output file names + correct typo * 🐛 FIX: Remove bamtools/split module from isoseq3/cluster * 🐛 FIX: Update output filename pattern input filename and output filename were the same * 👌 IMPROVE: Update meta.yml
This commit is contained in:
Sébastien Guizard
GitHub
parent
c912117972
commit
1cf207a5b6
3 changed files with 50 additions and 49 deletions
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@ -22,19 +22,20 @@ process ISOSEQ3_CLUSTER {
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tuple val(meta), path(bam)
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tuple val(meta), path(bam)
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output:
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output:
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tuple val(meta), path("*.bam") , emit: bam
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tuple val(meta), path("*.transcripts.bam") , emit: bam
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tuple val(meta), path("*.bam.pbi") , emit: pbi
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tuple val(meta), path("*.transcripts.bam.pbi") , emit: pbi
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tuple val(meta), path("*.cluster") , emit: cluster
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tuple val(meta), path("*.transcripts.cluster") , emit: cluster
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tuple val(meta), path("*.cluster_report.csv"), emit: cluster_report
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tuple val(meta), path("*.transcripts.cluster_report.csv"), emit: cluster_report
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tuple val(meta), path("*.transcriptset.xml") , emit: transcriptset
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tuple val(meta), path("*.transcripts.transcriptset.xml") , emit: transcriptset
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tuple val(meta), path("*.hq.bam") , emit: hq_bam
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path "versions.yml" , emit: versions
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tuple val(meta), path("*.hq.bam.pbi") , emit: hq_pbi
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tuple val(meta), path("*.lq.bam") , emit: lq_bam
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tuple val(meta), path("*.transcripts.hq.bam") , optional: true, emit: hq_bam
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tuple val(meta), path("*.lq.bam.pbi") , emit: lq_pbi
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tuple val(meta), path("*.transcripts.hq.bam.pbi") , optional: true, emit: hq_pbi
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path "versions.yml" , emit: versions
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tuple val(meta), path("*.transcripts.lq.bam") , optional: true, emit: lq_bam
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tuple val(meta), path("*.transcripts.lq.bam.pbi") , optional: true, emit: lq_pbi
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tuple val(meta), path("*.transcripts.singletons.bam") , optional: true, emit: singletons_bam
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tuple val(meta), path("*.transcripts.singletons.bam.pbi"), optional: true, emit: singletons_pbi
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tuple val(meta), path("*.singletons.bam") , optional: true, emit: singletons_bam
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tuple val(meta), path("*.singletons.bam.pbi"), optional: true, emit: singletons_pbi
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script:
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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@ -42,7 +43,7 @@ process ISOSEQ3_CLUSTER {
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isoseq3 \\
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isoseq3 \\
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cluster \\
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cluster \\
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$bam \\
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$bam \\
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${prefix}.bam \\
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${prefix}.transcripts.bam \\
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$options.args
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$options.args
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cat <<-END_VERSIONS > versions.yml
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cat <<-END_VERSIONS > versions.yml
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@ -35,47 +35,47 @@ output:
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- bam:
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- bam:
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type: file
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type: file
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description: BAM file of clustered consensus
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description: BAM file of clustered consensus
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pattern: "*.bam"
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pattern: "*.transcripts.bam"
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- pbi:
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- pbi:
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type: file
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type: file
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description: Pacbio Index of consensus reads generated by clustering
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description: Pacbio Index of consensus reads generated by clustering
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pattern: "*.pbi"
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pattern: "*.transcripts.bam.pbi"
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- cluster:
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- cluster:
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type: file
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type: file
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description: A two columns (from, to) file describing original read name to new read name
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description: A two columns (from, to) file describing original read name to new read name
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pattern: "*.cluster"
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pattern: "*.transcripts.cluster"
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- cluster_report:
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- cluster_report:
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type: file
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type: file
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description: A table files clusters (transcripts) members (read)
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description: A table files clusters (transcripts) members (read)
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pattern: "*.cluster_report.csv"
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pattern: "*.transcripts.cluster_report.csv"
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- transcriptset:
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- transcriptset:
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type: file
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type: file
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description: A metadata xml file which contains full paths to data files
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description: A metadata xml file which contains full paths to data files
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pattern: "*.clustered.transcriptset.xml"
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pattern: "*.transcripts.transcriptset.xml"
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- hq_bam:
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- hq_bam:
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type: file
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type: file
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description: High quality reads
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description: High quality reads (when --use-qvs is set)
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pattern: "*.hq.bam"
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pattern: "*.transcripts.hq.bam"
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- hq_pbi:
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- hq_pbi:
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type: file
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type: file
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description: Pacbio index of high quality reads
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description: Pacbio index of high quality reads (when --use-qvs is set)
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pattern: "*.hq.bam.pbi"
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pattern: "*.transcripts.hq.bam.pbi"
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- lq_bam:
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- lq_bam:
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type: file
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type: file
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description: Low quality reads
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description: Low quality reads (when --use-qvs is set)
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pattern: "*.lq.bam"
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pattern: "*.transcripts.lq.bam"
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- lq_pbi:
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- lq_pbi:
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type: file
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type: file
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description: Pacbio index of low quality reads
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description: Pacbio index of low quality reads (when --use-qvs is set)
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pattern: "*.lq.bam.pbi"
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pattern: "*.transcripts.lq.bam.pbi"
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- singletons_bam:
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- singletons_bam:
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type: file
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type: file
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description: Unclustered reads
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description: Unclustered reads (when --singletons is set)
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pattern: "*.singletons.bam"
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pattern: "*.transcripts.singletons.bam"
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- singletons_pbi:
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- singletons_pbi:
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type: file
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type: file
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description: Pacbio index of unclustered reads
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description: Pacbio index of unclustered reads (when --singletons is set)
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pattern: "*.singletons.bam.pbi"
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pattern: "*.transcripts.singletons.bam.pbi"
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authors:
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authors:
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- "@sguizard"
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- "@sguizard"
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@ -4,25 +4,25 @@
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- isoseq3
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- isoseq3
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- isoseq3/cluster
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- isoseq3/cluster
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files:
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files:
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- path: output/isoseq3/test.bam
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- path: output/isoseq3/test.transcripts.bam
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md5sum: ca8277f4d8fe1bba68ba266c42b46dd1
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md5sum: eb36697688099c757ef4196f54ad7d7a
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- path: output/isoseq3/test.bam.pbi
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- path: output/isoseq3/test.transcripts.bam.pbi
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md5sum: cbc06657b4543faba7ff886b3b12b862
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md5sum: db70cee03421822e9b8f9fb6b228f461
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- path: output/isoseq3/test.cluster
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- path: output/isoseq3/test.transcripts.cluster
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md5sum: d5059d856763fc5591332980bfc0d57b
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md5sum: d5059d856763fc5591332980bfc0d57b
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- path: output/isoseq3/test.cluster_report.csv
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- path: output/isoseq3/test.transcripts.cluster_report.csv
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md5sum: 342d97dc10aedf80a45977edcb491c62
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md5sum: 342d97dc10aedf80a45977edcb491c62
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- path: output/isoseq3/test.hq.bam
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- path: output/isoseq3/test.transcripts.hq.bam
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md5sum: e93ea85776c35c246364d954032c2ea9
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md5sum: 4c5f4ffb429107c9c9578419e07d6987
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- path: output/isoseq3/test.hq.bam.pbi
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- path: output/isoseq3/test.transcripts.hq.bam.pbi
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md5sum: 5a8ea7668e8f8e173478b28cbb6ab515
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md5sum: 39ac3e957c8d55b0ce3f425d63baa154
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- path: output/isoseq3/test.lq.bam
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- path: output/isoseq3/test.transcripts.lq.bam
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md5sum: 4ea0e4f4a6cc689dcc275adcdf688fad
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md5sum: 710ca4bc58ac039d76775460e1c822a0
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- path: output/isoseq3/test.lq.bam.pbi
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- path: output/isoseq3/test.transcripts.lq.bam.pbi
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md5sum: f5edc24711b2c8d6474d60cb69022af0
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md5sum: 9b32036553bf3dced3065e6d0f36aef9
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- path: output/isoseq3/test.singletons.bam
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- path: output/isoseq3/test.transcripts.singletons.bam
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md5sum: 73d131920bd42e1fc5fca2e6cb71f4b2
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md5sum: 0288577406b9d1e7356de9b4d7c2bb7c
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- path: output/isoseq3/test.singletons.bam.pbi
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- path: output/isoseq3/test.transcripts.singletons.bam.pbi
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md5sum: 73980863be4b5bda2846325c737f0b5e
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md5sum: 8e0e0681179c0c36209b49fa60783841
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- path: output/isoseq3/test.transcriptset.xml
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- path: output/isoseq3/test.transcripts.transcriptset.xml
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contains: [ 'PacBio.DataSet.TranscriptSet' ]
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contains: [ 'PacBio.DataSet.TranscriptSet' ]
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