From 81d4e3b60583aea219693d5ba1e6b4fb9ee0b901 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Langer?=
 <61791748+bjlang@users.noreply.github.com>
Date: Wed, 6 Sep 2023 16:05:41 +0200
Subject: [PATCH] Include csi support and resolve conflicts in atacseq.nf

---
 workflows/atacseq.nf | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/workflows/atacseq.nf b/workflows/atacseq.nf
index d4da4778..3bbc92fb 100644
--- a/workflows/atacseq.nf
+++ b/workflows/atacseq.nf
@@ -181,7 +181,6 @@ workflow ATACSEQ {
     // SUBWORKFLOW: Alignment with BWA & BAM QC
     //
     ch_genome_bam        = Channel.empty()
-    ch_genome_bam_index  = Channel.empty()
     ch_samtools_stats    = Channel.empty()
     ch_samtools_flagstat = Channel.empty()
     ch_samtools_idxstats = Channel.empty()
@@ -193,7 +192,6 @@ workflow ATACSEQ {
             PREPARE_GENOME.out.fasta
         )
         ch_genome_bam        = FASTQ_ALIGN_BWA.out.bam
-        ch_genome_bam_index  = FASTQ_ALIGN_BWA.out.bai
         ch_samtools_stats    = FASTQ_ALIGN_BWA.out.stats
         ch_samtools_flagstat = FASTQ_ALIGN_BWA.out.flagstat
         ch_samtools_idxstats = FASTQ_ALIGN_BWA.out.idxstats
@@ -212,7 +210,6 @@ workflow ATACSEQ {
             PREPARE_GENOME.out.fasta
         )
         ch_genome_bam        = FASTQ_ALIGN_BOWTIE2.out.bam
-        ch_genome_bam_index  = FASTQ_ALIGN_BOWTIE2.out.bai
         ch_samtools_stats    = FASTQ_ALIGN_BOWTIE2.out.stats
         ch_samtools_flagstat = FASTQ_ALIGN_BOWTIE2.out.flagstat
         ch_samtools_idxstats = FASTQ_ALIGN_BOWTIE2.out.idxstats
@@ -265,7 +262,6 @@ workflow ATACSEQ {
             [],
             []
         )
-        ch_genome_bam_index  = FASTQ_ALIGN_CHROMAP.out.bai
         ch_genome_bam        = FASTQ_ALIGN_CHROMAP.out.bam
         ch_samtools_stats    = FASTQ_ALIGN_CHROMAP.out.stats
         ch_samtools_flagstat = FASTQ_ALIGN_CHROMAP.out.flagstat
@@ -285,7 +281,6 @@ workflow ATACSEQ {
             params.seq_center ?: ''
         )
         ch_genome_bam        = ALIGN_STAR.out.bam
-        ch_genome_bam_index  = ALIGN_STAR.out.bai
         ch_samtools_stats    = ALIGN_STAR.out.stats
         ch_samtools_flagstat = ALIGN_STAR.out.flagstat
         ch_samtools_idxstats = ALIGN_STAR.out.idxstats
@@ -395,6 +390,7 @@ workflow ATACSEQ {
 
         ch_merged_library_filter_bam = MERGED_LIBRARY_BAM_SHIFT_READS.out.bam
         ch_merged_library_filter_bai = MERGED_LIBRARY_BAM_SHIFT_READS.out.bai
+        ch_merged_library_filter_csi = MERGED_LIBRARY_BAM_SHIFT_READS.out.csi
         ch_merged_library_filter_flagstat = MERGED_LIBRARY_BAM_SHIFT_READS.out.flagstat
     }
 
@@ -423,7 +419,16 @@ workflow ATACSEQ {
 
     // Create channels: [ meta, [bam], [bai] ] or [ meta, [ bam, control_bam ] [ bai, control_bai ] ]
     ch_merged_library_filter_bam
-        .join(ch_merged_library_filter_bai, by: [0])
+        .join(ch_merged_library_filter_bai, by: [0], remainder: true)
+        .join(ch_merged_library_filter_csi, by: [0], remainder: true)
+        .map {
+            meta, bam, bai, csi ->
+                if (bai) {
+                    [ meta, bam, bai ]
+                } else {
+                    [ meta, bam, csi ]
+                }
+        }
         .set { ch_bam_bai }
 
     if (params.with_control) {