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Include csi support and resolve conflicts in atacseq.nf #2

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Include csi support and resolve conflicts in atacseq.nf #2

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17 changes: 11 additions & 6 deletions workflows/atacseq.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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()
Expand All @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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
}

Expand Down Expand Up @@ -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) {
Expand Down