Commit 2d53d37c authored by Brandi Cantarel's avatar Brandi Cantarel

update pe/se trim/rna_align

parent 36711f28
Pipeline #8069 failed with stage
in 2 seconds
......@@ -61,13 +61,13 @@ if (params.pairs == 'pe') {
spltnames
.splitCsv()
.filter { fileMap.get(it[1]) != null & fileMap.get(it[2]) != null }
.map { it -> tuple(it[0], [fileMap.get(it[1]), fileMap.get(it[2])]) }
.map { it -> tuple(it[0], ([fileMap.get(it[1]), fileMap.get(it[2])])) }
.set { read }
} else {
spltnames
.splitCsv()
.filter { fileMap.get(it[1]) != null }
.map { it -> tuple(it[0], [fileMap.get(it[1])]) }
.map { it -> tuple(it[0], ([fileMap.get(it[1])])) }
.set { read }
}
if( ! read ) { error "Didn't match any input files with entries in the design file" }
......@@ -78,46 +78,25 @@ process trim {
input:
set pair_id, file(fqs) from read
output:
set pair_id, file("${pair_id}.trim.R1.fastq.gz"),file("${pair_id}.trim.R2.fastq.gz") into trimread
set pair_id, file("${pair_id}.trim.R1.fastq.gz"),file("${pair_id}.trim.R2.fastq.gz") into fusionfq
set pair_id, file("${pair_id}.trim.R*.fastq.gz") into trimread
script:
"""
bash $baseDir/process_scripts/preproc_fastq/trimgalore.sh -f -p ${pair_id} ${fqs}
"""
}
// Align trimmed reads to genome indes with hisat2
// Sort and index with samtools
// QC aligned reads with fastqc
// Alignment stats with samtools
process starfusion {
errorStrategy 'ignore'
publishDir "$params.output", mode: 'copy'
input:
set pair_id, file(fq1), file(fq2) from fusionfq
output:
file("${pair_id}.starfusion.txt") into fusionout
when:
params.fusion == 'detect' && params.pairs == 'pe'
script:
"""
bash $baseDir/process_scripts/alignment/starfusion.sh -p ${pair_id} -r ${index_path} -a ${fq1} -b ${fq2} -m trinity -f
"""
}
process align {
errorStrategy 'ignore'
publishDir "$params.output", mode: 'copy'
input:
set pair_id, file(fq1), file(fq2) from trimread
set pair_id, file(fqs) from trimread
output:
set pair_id, file("${pair_id}.bam") into aligned
set pair_id, file("${pair_id}.bam") into aligned2
file("${pair_id}.alignerout.txt") into hsatout
script:
"""
bash $baseDir/process_scripts/alignment/rnaseqalign.sh -a $params.align -p ${pair_id} -r ${index_path} -x ${fq1} -y ${fq2}
bash $baseDir/process_scripts/alignment/rnaseqalign.sh -a $params.align -p ${pair_id} -r ${index_path} ${fqs}
"""
}
......@@ -135,23 +114,7 @@ process alignqc {
"""
}
// Summarize all flagstat output
process parse_alignstat {
publishDir "$params.output", mode: 'copy'
input:
file(txt) from alignstats.toList()
file(txt) from hsatout.toList()
output:
file('alignment.summary.txt')
script:
"""
perl $baseDir/scripts/parse_flagstat.pl *.flagstat.txt
"""
}
// Identify duplicate reads with Picard
process markdups {
publishDir "$params.output", mode: 'copy'
input:
......@@ -167,7 +130,6 @@ process markdups {
// Read summarization with subread
// Assemble transcripts with stringtie
process geneabund {
errorStrategy 'ignore'
publishDir "$params.output", mode: 'copy'
......
Subproject commit 529fdbfc477dcb0d2c5879e82f6175ea1dae818c
Subproject commit 96bcf78802267e8bb1834c06ffb98c5d700273e3
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