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Rationalise sorted bam/bai publishing #85

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merged 6 commits into from
Jan 24, 2025
Merged

Rationalise sorted bam/bai publishing #85

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e8d9cab
Rationalise sorted bam/bai publishing
pinin4fjords Jan 23, 2025
c246fb7
Correct some publish paths for files after UMI dedup
pinin4fjords Jan 23, 2025
5a3a56b
update snap
pinin4fjords Jan 23, 2025
fc57c29
Remove variable files from snap
pinin4fjords Jan 23, 2025
51e1021
Fix snap
pinin4fjords Jan 23, 2025
24514c0
Update CHANGELOG.md
pinin4fjords Jan 23, 2025
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58 changes: 9 additions & 49 deletions conf/modules.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -400,52 +400,23 @@ if (!params.skip_alignment) {
]
}

withName: 'NFCORE_RIBOSEQ:RIBOSEQ:.*:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT' {
ext.prefix = { "${meta.id}.genome.sorted" }
withName: 'NFCORE_RIBOSEQ:RIBOSEQ:.*:BAM_SORT_STATS_SAMTOOLS_(GEN|TRANSCRIPT)OME:SAMTOOLS_(SORT|INDEX)' {
publishDir = [
path: { "${params.outdir}/alignment/${params.aligner}/sorted" },
mode: params.publish_dir_mode,
pattern: "*.bam",
pattern: "*.{bam,bai,csi}",
saveAs: { ( ['star'].contains(params.aligner) &&
( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
) || params.save_align_intermeds || params.skip_markduplicates ? it : null }
]
}

withName: 'NFCORE_RIBOSEQ:RIBOSEQ:.*:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT' {
withName: 'NFCORE_RIBOSEQ:RIBOSEQ:.*:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_(SORT|INDEX)' {
ext.prefix = { "${meta.id}.transcriptome.sorted" }
publishDir = [
path: { "${params.outdir}/alignment/${params.aligner}/sorted" },
mode: params.publish_dir_mode,
pattern: "*.bam",
saveAs: { ( ['star'].contains(params.aligner) &&
( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
) || params.save_align_intermeds || params.skip_markduplicates ? it : null }
]
}

withName: 'NFCORE_RIBOSEQ:RIBOSEQ:.*:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX' {
ext.args = { params.bam_csi_index ? '-c' : '' }
publishDir = [
path: { "${params.outdir}/alignment/${params.aligner}/sorted" },
mode: params.publish_dir_mode,
pattern: "*.{bai,csi}",
saveAs: { ( ['star'].contains(params.aligner) &&
( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
) || params.save_align_intermeds || params.skip_markduplicates ? it : null }
]
}

withName: 'NFCORE_RIBOSEQ:RIBOSEQ:.*:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX' {
ext.args = { params.bam_csi_index ? '-c' : '' }
publishDir = [
path: { "${params.outdir}/alignment/${params.aligner}/sorted" },
mode: params.publish_dir_mode,
pattern: "*.{bai,csi}",
saveAs: { ( ['star'].contains(params.aligner) &&
( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
) || params.save_align_intermeds || params.skip_markduplicates ? it : null }
]
withName: 'NFCORE_RIBOSEQ:RIBOSEQ:.*:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_(SORT|INDEX)' {
ext.prefix = { "${meta.id}.genome.sorted" }
}
}

Expand Down Expand Up @@ -533,17 +504,6 @@ if (!params.skip_alignment && params.aligner == 'star') {
]
}

withName: '.*:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX' {
publishDir = [
[
path: { params.save_align_intermeds ? "${params.outdir}/alignment/${params.aligner}/original" : params.outdir },
mode: params.publish_dir_mode,
pattern: '*.{bai.csi}',
saveAs: { params.save_align_intermeds ? it : null }
]
]
}

withName: '.*:QUANTIFY_STAR_SALMON:SALMON_QUANT' {
ext.args = { params.extra_salmon_quant_args ?: '' }
publishDir = [
Expand Down Expand Up @@ -666,9 +626,9 @@ if (!params.skip_alignment && params.aligner == 'star') {

withName: 'NFCORE_RIBOSEQ:RIBOSEQ:BAM_DEDUP_UMI:SAMTOOLS_SORT' {
ext.args = '-n'
ext.prefix = { "${meta.id}.umi_dedup.transcriptome" }
ext.prefix = { "${meta.id}.umi_dedup.transcriptome.namesorted" }
publishDir = [
path: { "${params.outdir}/alignment/${params.aligner}/sorted" },
path: { "${params.outdir}/alignment/${params.aligner}/deduplicated" },
mode: params.publish_dir_mode,
pattern: '*.bam',
saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
Expand All @@ -695,7 +655,7 @@ if (!params.skip_alignment && params.aligner == 'star') {
withName: 'NFCORE_RIBOSEQ:RIBOSEQ:BAM_DEDUP_UMI:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
ext.prefix = { "${meta.id}.transcriptome.sorted" }
publishDir = [
path: { "${params.outdir}/alignment/${params.aligner}/sorted" },
path: { "${params.outdir}/alignment/${params.aligner}/deduplicated" },
mode: params.publish_dir_mode,
pattern: '*.bam',
saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
Expand All @@ -704,7 +664,7 @@ if (!params.skip_alignment && params.aligner == 'star') {

withName: 'NFCORE_RIBOSEQ:RIBOSEQ:BAM_DEDUP_UMI:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
publishDir = [
path: { "${params.outdir}/alignment/${params.aligner}/sorted" },
path: { "${params.outdir}/alignment/${params.aligner}/deduplicated" },
mode: params.publish_dir_mode,
pattern: '*.bai',
saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
Expand Down
7 changes: 5 additions & 2 deletions tests/.nftignore
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
alignment/star/**/*.bam.stats
alignment/star/**/*.{bam,bam.bai}
alignment/star/deduplicated/umicollapse/*_UMICollapse.log
alignment/star/log/*.Log.{final.out,out,progress.out}
multiqc/star/multiqc.log
multiqc/star/multiqc_general_stats.txt
Expand All @@ -14,9 +15,11 @@ multiqc/star/multiqc_report_data/multiqc_sources.txt
multiqc/star/multiqc_report_plots/{svg,pdf,png}/*.{svg,pdf,png}
pipeline_info/*.{html,json,txt,yml}
preprocessing/fastqc/*_fastqc.{html,zip}
preprocessing/fq_lint/**/*.fq_lint.txt
preprocessing/sortmerna/*.sortmerna.log
preprocessing/trimgalore/*.fastq.gz_trimming_report.txt
preprocessing/trimgalore/fastqc/*_fastqc.{html,zip}
preprocessing/umitools/*.umi_extract.log
quantification/salmon/*/aux_info/ambig_info.tsv
quantification/salmon/*/aux_info/fld.gz
quantification/salmon/*/aux_info/meta_info.json
Expand All @@ -37,5 +40,5 @@ quantification/salmon/salmon.merged.transcript_counts.tsv
quantification/salmon/salmon.merged.transcript_lengths.tsv
quantification/salmon/salmon.merged.transcript_tpm.tsv
riboseq_qc/ribotish/*_qual.pdf
preprocessing/umitools/*.umi_extract.log
alignment/star/deduplicated/umicollapse/*_UMICollapse.log
translational_efficiency/anota2seq/*.{jpeg,jpg,png,pdf,rds,tsv}
translational_efficiency/anota2seq/*.{buffering,total_mRNA,translated_mRNA,translation}.anota2seq.results.tsv
56 changes: 15 additions & 41 deletions tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -173,39 +173,51 @@
"alignment/star/sorted/SRX11780879.genome.sorted.bam",
"alignment/star/sorted/SRX11780879.genome.sorted.bam.bai",
"alignment/star/sorted/SRX11780879.transcriptome.sorted.bam",
"alignment/star/sorted/SRX11780879.transcriptome.sorted.bam.bai",
"alignment/star/sorted/SRX11780880.genome.sorted.bam",
"alignment/star/sorted/SRX11780880.genome.sorted.bam.bai",
"alignment/star/sorted/SRX11780880.transcriptome.sorted.bam",
"alignment/star/sorted/SRX11780880.transcriptome.sorted.bam.bai",
"alignment/star/sorted/SRX11780881.genome.sorted.bam",
"alignment/star/sorted/SRX11780881.genome.sorted.bam.bai",
"alignment/star/sorted/SRX11780881.transcriptome.sorted.bam",
"alignment/star/sorted/SRX11780881.transcriptome.sorted.bam.bai",
"alignment/star/sorted/SRX11780882.genome.sorted.bam",
"alignment/star/sorted/SRX11780882.genome.sorted.bam.bai",
"alignment/star/sorted/SRX11780882.transcriptome.sorted.bam",
"alignment/star/sorted/SRX11780882.transcriptome.sorted.bam.bai",
"alignment/star/sorted/SRX11780883.genome.sorted.bam",
"alignment/star/sorted/SRX11780883.genome.sorted.bam.bai",
"alignment/star/sorted/SRX11780883.transcriptome.sorted.bam",
"alignment/star/sorted/SRX11780883.transcriptome.sorted.bam.bai",
"alignment/star/sorted/SRX11780884.genome.sorted.bam",
"alignment/star/sorted/SRX11780884.genome.sorted.bam.bai",
"alignment/star/sorted/SRX11780884.transcriptome.sorted.bam",
"alignment/star/sorted/SRX11780884.transcriptome.sorted.bam.bai",
"alignment/star/sorted/SRX11780885.genome.sorted.bam",
"alignment/star/sorted/SRX11780885.genome.sorted.bam.bai",
"alignment/star/sorted/SRX11780885.transcriptome.sorted.bam",
"alignment/star/sorted/SRX11780885.transcriptome.sorted.bam.bai",
"alignment/star/sorted/SRX11780886.genome.sorted.bam",
"alignment/star/sorted/SRX11780886.genome.sorted.bam.bai",
"alignment/star/sorted/SRX11780886.transcriptome.sorted.bam",
"alignment/star/sorted/SRX11780886.transcriptome.sorted.bam.bai",
"alignment/star/sorted/SRX11780887.genome.sorted.bam",
"alignment/star/sorted/SRX11780887.genome.sorted.bam.bai",
"alignment/star/sorted/SRX11780887.transcriptome.sorted.bam",
"alignment/star/sorted/SRX11780887.transcriptome.sorted.bam.bai",
"alignment/star/sorted/SRX11780888.genome.sorted.bam",
"alignment/star/sorted/SRX11780888.genome.sorted.bam.bai",
"alignment/star/sorted/SRX11780888.transcriptome.sorted.bam",
"alignment/star/sorted/SRX11780888.transcriptome.sorted.bam.bai",
"alignment/star/sorted/SRX11780889.genome.sorted.bam",
"alignment/star/sorted/SRX11780889.genome.sorted.bam.bai",
"alignment/star/sorted/SRX11780889.transcriptome.sorted.bam",
"alignment/star/sorted/SRX11780889.transcriptome.sorted.bam.bai",
"alignment/star/sorted/SRX11780890.genome.sorted.bam",
"alignment/star/sorted/SRX11780890.genome.sorted.bam.bai",
"alignment/star/sorted/SRX11780890.transcriptome.sorted.bam",
"alignment/star/sorted/SRX11780890.transcriptome.sorted.bam.bai",
"alignment/star/sorted/samtools_stats",
"alignment/star/sorted/samtools_stats/SRX11780879.genome.sorted.bam.flagstat",
"alignment/star/sorted/samtools_stats/SRX11780879.genome.sorted.bam.idxstats",
Expand Down Expand Up @@ -991,30 +1003,6 @@
"allsamples_all.txt:md5,fcdb19d5389596185db2ebce2663cd94",
"allsamples_pred.txt:md5,fcdb19d5389596185db2ebce2663cd94",
"allsamples_transprofile.py:md5,10add18b7c9d626042b8980ee896adb9",
"SRX11780879.fq_lint.txt:md5,aabe1c97f1cfe8ba39cf3f156cb01f58",
"SRX11780880.fq_lint.txt:md5,0391a552cb94185b9fd0dc6b9dde94c8",
"SRX11780881.fq_lint.txt:md5,344a09865afb4a5af720c8da01371f25",
"SRX11780882.fq_lint.txt:md5,6ca568f9ba4b134d4be4d05771bee404",
"SRX11780883.fq_lint.txt:md5,91b4d7a63566095b5e736cdf52840ae9",
"SRX11780884.fq_lint.txt:md5,f091b7901f29bd4c89a3717e9f7c1a61",
"SRX11780885.fq_lint.txt:md5,9a81835ac9390e8199898865328bfadc",
"SRX11780886.fq_lint.txt:md5,1df2f1af4224ac21e1cdd0def180cced",
"SRX11780887.fq_lint.txt:md5,849506abd4f29833739369f3f0922d70",
"SRX11780888.fq_lint.txt:md5,57d0586019d717210a6892620857031d",
"SRX11780889.fq_lint.txt:md5,dbed4006c1781c862cbd699a726b6236",
"SRX11780890.fq_lint.txt:md5,36fa69af262899ce9b509724aef54654",
"SRX11780879.fq_lint.txt:md5,00e5a9aedf23dcb2575f2936737f9a15",
"SRX11780880.fq_lint.txt:md5,46c9ad0b5f6048056149075e6a1fe1fb",
"SRX11780881.fq_lint.txt:md5,b10044592d9cf154c690183bbfcf18b0",
"SRX11780882.fq_lint.txt:md5,15bfe17f721c914461e495f22f4b82ee",
"SRX11780883.fq_lint.txt:md5,9f893d53e00c9948c1712a3fd70fc9ef",
"SRX11780884.fq_lint.txt:md5,72bb432acad23581f954bf90a09ce04c",
"SRX11780885.fq_lint.txt:md5,2be4014900bf0af0fdab87a942d54d49",
"SRX11780886.fq_lint.txt:md5,792f20f963edff8dc581780340608d3b",
"SRX11780887.fq_lint.txt:md5,999dc7c82cd5522dff04e33fd21a487d",
"SRX11780888.fq_lint.txt:md5,663e2bda4c1fee45c65d59fe3a45a5cd",
"SRX11780889.fq_lint.txt:md5,5bc42250cad100a94be2c10c910a1990",
"SRX11780890.fq_lint.txt:md5,ebdb0558c9fc3d38a93447efff2acfe2",
"expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
"observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
"observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
Expand Down Expand Up @@ -1080,27 +1068,13 @@
"SRX11780889_qual.txt:md5,4c567c2c47eb52bf81e514a39eb5a695",
"SRX11780890.para.py:md5,5f1696c5bf20116fa63363917e131284",
"SRX11780890_qual.txt:md5,0f761538ecafb2718bd781c6e1fb7dc1",
"treated_vs_control.Anota2seqDataSet.rds:md5,ee24bd4d304465d9cfedd731c0c18db4",
"treated_vs_control.R_sessionInfo.log:md5,3623a50b4668bfebf502bf7080800996",
"treated_vs_control.buffering.anota2seq.results.tsv:md5,7e653c310ee57b9d8b2e95fd93071f25",
"treated_vs_control.fold_change.png:md5,75b225afa14bf36496a6c15aed67bb9c",
"treated_vs_control.interaction_p_distribution.pdf:md5,1151537872a2cddd40f4bd4cd06365ef",
"treated_vs_control.mRNA_abundance.anota2seq.results.tsv:md5,68b329da9893e34099c7d8ad5cb9c940",
"treated_vs_control.residual_distribution_summary.jpeg:md5,50601ad5e8a86491b64d5749c367d06a",
"treated_vs_control.residual_vs_fitted.jpeg:md5,e6b76323d717847b2d729ff6fc7cb300",
"treated_vs_control.rvm_fit_for_all_contrasts_group.jpg:md5,916343be0d369b3514b7224acb23ffb5",
"treated_vs_control.rvm_fit_for_interactions.jpg:md5,87e4a8a5258957946593cf6e886e67d9",
"treated_vs_control.rvm_fit_for_omnibus_group.jpg:md5,379731ad9cb5169194347ad8f5ef8d77",
"treated_vs_control.simulated_vs_obt_dfbetas_without_interaction.pdf:md5,29c180ee3577ee4d84fe23ab9392bcf8",
"treated_vs_control.total_mRNA.anota2seq.results.tsv:md5,18ab49d35b0977d311cdac26fc3ee365",
"treated_vs_control.translated_mRNA.anota2seq.results.tsv:md5,cfb7040afa122749d6110538e40f1d87",
"treated_vs_control.translation.anota2seq.results.tsv:md5,a4bfdd6ad0ff6f75d7ba1ff5bd7d2b35"
"treated_vs_control.R_sessionInfo.log:md5,3623a50b4668bfebf502bf7080800996"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.3"
"nextflow": "24.10.4"
},
"timestamp": "2024-12-20T17:38:38.869311163"
"timestamp": "2025-01-23T17:23:55.759142246"
}
}
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