Fix nf-core#931

drpatelh · Mar 16, 2023 · 07ddd71 · 07ddd71
1 parent a8f53be
commit 07ddd71
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Enhancements & fixes
 
 - [[#878](https://github.com/nf-core/rnaseq/pull/878)] - Allow tabs in fasta header when creating decoys for salmon index
+- [[#931](https://github.com/nf-core/rnaseq/pull/931)] - Save transcriptome BAM files when using `--save_umi_intermeds` / `--save_align_intermeds`
 - [[#934](https://github.com/nf-core/rnaseq/pull/934)] - Union of `ext.args` and `params.extra_star_align_args` prevents parameter clashes in the STAR module
 - [[#940](https://github.com/nf-core/rnaseq/issues/940)] - Bugfix in `salmon_summarizedexperiment.r` to ensure `rbind` doesn't fail when `rowdata` has no `tx` column. See ([[#941](https://github.com/nf-core/rnaseq/pull/941)]) for details.
 - [[#944](https://github.com/nf-core/rnaseq/issues/944)] - Read clipping using clip_r1, clip_r2, three_prime_clip_r1, three_prime_clip_r2 disabled in 3.10

diff --git a/conf/modules.config b/conf/modules.config
@@ -595,39 +595,70 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                 ext.prefix = { "${meta.id}.umi_dedup.transcriptome" }
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}" },
-                    enabled: false
+                    mode: params.publish_dir_mode,
+                    pattern: '*.bam',
+                    enabled: (
+                        params.save_align_intermeds ||
+                        params.save_umi_intermeds
+                    )
                 ]
             }
 
             withName: 'NFCORE_RNASEQ:RNASEQ:UMITOOLS_PREPAREFORSALMON' {
                 ext.prefix = { "${meta.id}.umi_dedup.transcriptome.filtered" }
                 publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/umitools/log" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.log'
+                    [
+                        path: { "${params.outdir}/${params.aligner}/umitools/log" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.log'
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.aligner}" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.bam',
+                        enabled: (
+                            params.save_align_intermeds ||
+                            params.save_umi_intermeds
+                        )
+                    ]
                 ]
             }
 
             withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
                 ext.prefix = { "${meta.id}.transcriptome.sorted" }
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}" },
-                    enabled: false
+                    mode: params.publish_dir_mode,
+                    pattern: '*.bam',
+                    enabled: (
+                        params.save_align_intermeds ||
+                        params.save_umi_intermeds
+                    )
                 ]
             }
 
             withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}" },
-                    enabled: false
+                    mode: params.publish_dir_mode,
+                    pattern: '*.bai',
+                    enabled: (
+                        params.save_align_intermeds ||
+                        params.save_umi_intermeds
+                    )
                 ]
             }
 
             withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
                 ext.prefix = { "${meta.id}.transcriptome.sorted.bam" }
                 publishDir = [
-                    path: { "${params.outdir}/${params.aligner}" },
-                    enabled: false
+                    path: { "${params.outdir}/${params.aligner}/samtools_stats" },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.{stats,flagstat,idxstats}',
+                    enabled: (
+                        params.save_align_intermeds ||
+                        params.save_umi_intermeds
+                    )
                 ]
             }
 
@@ -639,16 +670,32 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                 ].join(' ').trim() }
                 ext.prefix = { "${meta.id}.umi_dedup.transcriptome.sorted" }
                 publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/umitools" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.tsv'
+                    [
+                        path: { "${params.outdir}/${params.aligner}/umitools" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.tsv'
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.aligner}" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.bam',
+                        enabled: (
+                            params.save_align_intermeds ||
+                            params.save_umi_intermeds
+                        )
+                    ]
                 ]
             }
 
             withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX' {
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}" },
-                    enabled: false
+                    mode: params.publish_dir_mode,
+                    pattern: '*.bai',
+                    enabled: (
+                        params.save_align_intermeds ||
+                        params.save_umi_intermeds
+                    )
                 ]
             }