corrected: BAM without PCR duplicates for stitchedpeaks (#120)

stjude · Jun 3, 2024 · d29ba17 · d29ba17
1 parent 091cf91
commit d29ba17
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Showing 6 changed files with 20 additions and 20 deletions.
diff --git a/peaseq-case.wdl b/peaseq-case.wdl
@@ -641,8 +641,8 @@ workflow peaseq {
     call rose.rose as SE_rose {
         input :
             gtffile=gtf,
-            bamfile=SE_mergebam_afterbklist,
-            bamindex=select_first([SE_merge_bklist.indexbam, SE_mergeindexstats.indexbam]),
+            bamfile=SE_merge_markdup.mkdupbam,
+            bamindex=SE_merge_mkdup.indexbam,
             bedfile_auto=SE_macs.peakbedfile,
             bedfile_all=SE_all.peakbedfile,
             default_location = if defined(results_name) then results_name + '/single-end_mode/PEAKS/STITCHED_peaks' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/PEAKS/STITCHED_peaks' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/PEAKS/STITCHED_peaks'
@@ -851,8 +851,8 @@ workflow peaseq {
     call rose.rose as PE_rose {
         input :
             gtffile=gtf,
-            bamfile=PE_sample_bam,
-            bamindex=select_first([PE_merge_bklist.indexbam, PE_mergeindexstats.indexbam, uno_PE_mapping.bklist_index, uno_PE_mapping.bam_index]),
+            bamfile=fraggraph.fragbamfile,
+            bamindex=frag_index.indexbam,
             bedfile_auto=PE_macs.peakbedfile,
             bedfile_all=PE_all.peakbedfile,
             default_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/PEAKS/STITCHED_peaks'

diff --git a/peaseq-control.wdl b/peaseq-control.wdl
@@ -1025,10 +1025,10 @@ workflow peaseq {
     call rose.rose as SE_rose {
         input :
             gtffile=gtf,
-            bamfile=SE_s_mergebam_afterbklist,
-            bamindex=select_first([SE_s_merge_bklist.indexbam, SE_s_mergeindexstats.indexbam]),
-            control=SE_c_mergebam_afterbklist,
-            controlindex=select_first([SE_c_merge_bklist.indexbam, SE_c_mergeindexstats.indexbam]),
+            bamfile=SE_s_merge_markdup.mkdupbam,
+            bamindex=SE_s_merge_mkdup.indexbam,
+            control=SE_c_merge_markdup.mkdupbam,
+            controlindex=SE_c_merge_mkdup.indexbam,
             bedfile_auto=SE_macs.peakbedfile,
             bedfile_all=SE_all.peakbedfile,
             default_location = if defined(results_name) then results_name + '/single-end_mode/PEAKS/STITCHED_peaks' else if multi_fastqpair then 'AllCases_' + length(sample_fastqfiles) + 'fastqpairs+control/single-end_mode/PEAKS/STITCHED_peaks' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '+control/single-end_mode/PEAKS/STITCHED_peaks'
@@ -1353,10 +1353,10 @@ workflow peaseq {
     call rose.rose as PE_rose {
         input :
             gtffile=gtf,
-            bamfile=PE_sample_bam,
-            bamindex=select_first([s_PE_merge_bklist.indexbam, s_PE_mergeindexstats.indexbam, s_uno_PE_mapping.bklist_index, s_uno_PE_mapping.bam_index]),
-            control=PE_control_bam,
-            controlindex=select_first([c_PE_merge_bklist.indexbam, c_PE_mergeindexstats.indexbam, c_uno_PE_mapping.bklist_index, c_uno_PE_mapping.bam_index]),
+            bamfile=s_fraggraph.fragbamfile,
+            bamindex=s_frag_index.indexbam,
+            control=c_fraggraph.fragbamfile,
+            controlindex=c_frag_index.indexbam,
             bedfile_auto=PE_macs.peakbedfile,
             bedfile_all=PE_all.peakbedfile,
             default_location=if defined(results_name) then results_name + '/PEAKS/STITCHED_peaks' else sub(basename(PE_sample_bam),'.sorted.b.*$','') + '+control/PEAKS/STITCHED_peaks'

diff --git a/seaseq-case.wdl b/seaseq-case.wdl
@@ -474,8 +474,8 @@ workflow seaseq {
     call rose.rose {
         input :
             gtffile=gtf,
-            bamfile=sample_bam,
-            bamindex=select_first([merge_bklist.indexbam, mergeindexstats.indexbam, mapping.bklist_index, mapping.bam_index]),
+            bamfile=select_first([merge_markdup.mkdupbam, mapping.mkdup_bam]),
+            bamindex=select_first([merge_mkdup.indexbam, mapping.mkdup_index]),
             bedfile_auto=macs.peakbedfile,
             bedfile_all=all.peakbedfile,
             default_location=sub(basename(sample_bam),'.sorted.b.*$','') + '/PEAKS/STITCHED_peaks'

diff --git a/seaseq-control.wdl b/seaseq-control.wdl
@@ -743,10 +743,10 @@ workflow seaseq {
     call rose.rose {
         input :
             gtffile=gtf,
-            bamfile=sample_bam,
-            bamindex=select_first([s_merge_bklist.indexbam, s_mergeindexstats.indexbam, s_mapping.bklist_index, s_mapping.bam_index]),
-            control=control_bam,
-            controlindex=select_first([c_merge_bklist.indexbam, c_mergeindexstats.indexbam, c_mapping.bklist_index, c_mapping.bam_index]),
+            bamfile=select_first([s_merge_markdup.mkdupbam, s_mapping.mkdup_bam]),
+            bamindex=select_first([s_merge_mkdup.indexbam, s_mapping.mkdup_index]),
+            control=select_first([c_merge_markdup.mkdupbam, c_mapping.mkdup_bam]),
+            controlindex=select_first([c_merge_mkdup.indexbam, c_mapping.mkdup_index]),
             bedfile_auto=macs.peakbedfile,
             bedfile_all=all.peakbedfile,
             default_location=if defined(results_name) then results_name + '/PEAKS/STITCHED_peaks' else sub(basename(sample_bam),'.sorted.b.*$','') + '+control/PEAKS/STITCHED_peaks'

diff --git a/test/README.md b/test/README.md
diff --git a/workflows/tasks/rose.wdl b/workflows/tasks/rose.wdl
@@ -136,8 +136,8 @@ task rose {
         # ROSE CALLER
         #
         ROSE_main.py \
-            ~{if defined(stitch) then "-s" + stitch else ""} \
-            ~{if defined(tss) then "-t" + tss else ""} \
+            ~{if defined(stitch) then "-s " + stitch else ""} \
+            ~{if defined(tss) then "-t " + tss else ""} \
             --custom genome_refseq.ucsc \
             -i unionpeaks.gff \
             -r ~{basename(bamfile)} \