Merged ktrns/master into ktrns/dev. Fixed nf-core#164 (4/5 bp shift), f…

…ixed nf-core#168 (write genome fa and fai for IGV), fixed nf-core#169 (peak calling).
ktrns · Jul 3, 2023 · f14eeb8 · f14eeb8
2 parents eb04c86 + df64c3a
commit f14eeb8
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Showing 12 changed files with 499 additions and 108 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -459,6 +459,37 @@ process {
         ]
     }
 
+    withName: '.*:MERGED_LIBRARY_BAM_SHIFT_READS:DEEPTOOLS_ALIGNMENTSIEVE' {
+        ext.args   = '--ATACshift'
+        ext.prefix = { "${meta.id}.mLb.clN.shifted" }
+        publishDir = [
+            path: { "${params.outdir}/${params.aligner}/merged_library/shifted_reads" },
+            mode: params.publish_dir_mode,
+            pattern: '*.bam',
+            enabled: params.save_align_intermeds
+        ]
+    }
+
+    withName: '.*:MERGED_LIBRARY_BAM_SHIFT_READS:SAMTOOLS_SORT' {
+        ext.prefix = { "${meta.id}.mLb.clN.shifted.sorted" }
+        publishDir = [
+            path: { "${params.outdir}/${params.aligner}/merged_library/shifted_reads" },
+            mode: params.publish_dir_mode,
+            pattern: '*.bam',
+            enabled: params.shift_reads
+        ]
+    }
+
+    withName: '.*:MERGED_LIBRARY_BAM_SHIFT_READS:SAMTOOLS_INDEX' {
+        ext.prefix = { "${meta.id}.mLb.clN.shifted.sorted" }
+        publishDir = [
+            path: { "${params.outdir}/${params.aligner}/merged_library/shifted_reads" },
+            mode: params.publish_dir_mode,
+            pattern: '*.bai',
+            enabled: params.shift_reads
+        ]
+    }
+
     withName: '.*:MERGED_LIBRARY_BAM_TO_BIGWIG:BEDTOOLS_GENOMECOV' {
         ext.args   = {
             [
@@ -590,9 +621,12 @@ if (!params.skip_plot_fingerprint) {
 process {
     withName: '.*:MERGED_LIBRARY_CALL_ANNOTATE_PEAKS:MACS2_CALLPEAK' {
         ext.args   = [
+            '--format BED',
             '--keep-dup all',
             '--nomodel',
-            params.narrow_peak      ? '' : "--broad --broad-cutoff ${params.broad_cutoff}",
+            '--shift -75',
+            '--extsize 150',
+            params.narrow_peak      ? '--call-summits' : "--broad --broad-cutoff ${params.broad_cutoff}",
             params.save_macs_pileup ? '--bdg --SPMR' : '',
             params.macs_pvalue      ? "--pvalue ${params.macs_pvalue}" : '',
             params.macs_fdr         ? "--qvalue ${params.macs_fdr}" : ''
@@ -784,6 +818,37 @@ if (!params.skip_merge_replicates) {
             ]
         }
 
+        withName: '.*:MERGED_REPLICATE_BAM_SHIFT_READS:DEEPTOOLS_ALIGNMENTSIEVE' {
+            ext.args   = '--ATACshift'
+            ext.prefix = { "${meta.id}.mRp.clN.shifted" }
+            publishDir = [
+                path: { "${params.outdir}/${params.aligner}/merged_replicate" },
+                mode: params.publish_dir_mode,
+                pattern: '*.bam',
+                enabled: params.save_align_intermeds
+            ]
+        }
+
+        withName: '.*:MERGED_REPLICATE_BAM_SHIFT_READS:SAMTOOLS_SORT' {
+            ext.prefix = { "${meta.id}.mRp.clN.shifted.sorted" }
+            publishDir = [
+                path: { "${params.outdir}/${params.aligner}/merged_replicate/shifted_reads" },
+                mode: params.publish_dir_mode,
+                pattern: '*.bam',
+                enabled: params.shift_reads
+            ]
+        }
+
+        withName: '.*:MERGED_REPLICATE_BAM_SHIFT_READS:SAMTOOLS_INDEX' {
+            ext.prefix = { "${meta.id}.mRp.clN.shifted.sorted" }
+            publishDir = [
+                path: { "${params.outdir}/${params.aligner}/merged_replicate/shifted_reads" },
+                mode: params.publish_dir_mode,
+                pattern: '*.bai',
+                enabled: params.shift_reads
+            ]
+        }
+
         withName: '.*:MERGED_REPLICATE_BAM_TO_BIGWIG:BEDTOOLS_GENOMECOV' {
             ext.args   = {
                 [
@@ -820,6 +885,7 @@ if (!params.skip_merge_replicates) {
     process {
         withName: '.*:MERGED_REPLICATE_CALL_ANNOTATE_PEAKS:MACS2_CALLPEAK' {
             ext.args   = [
+                '--format BED',
                 '--keep-dup all',
                 '--nomodel',
                 params.narrow_peak      ? '' : "--broad --broad-cutoff ${params.broad_cutoff}",
@@ -957,7 +1023,7 @@ if (!params.skip_igv) {
                 [
                     path: { "${params.outdir}/genome" },
                     mode: params.publish_dir_mode,
-                    pattern: '*.{fa,fasta}'
+                    pattern: '*.{fa,fasta,fai}'
                 ]
             ]
         }