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Remove input cardinality warning for endorS.py when no bam filtering #362

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Merged
apeltzer merged 3 commits into from
Mar 1, 2020
Merged

Remove input cardinality warning for endorS.py when no bam filtering #362

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587a79f
standardised some endings
jfy133 Mar 1, 2020
ac1e79a
Remove endorS.py warning input channel cardinality warning when not r…
jfy133 Mar 1, 2020
4b28865
Merge branch '2-1-0-prep' of github.com:jfy133/eager into 2-1-0-prep
jfy133 Mar 1, 2020
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26 changes: 15 additions & 11 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -1357,18 +1357,15 @@ process samtools_flagstat_after_filter {
* Step 4c: Keep unmapped/remove unmapped reads flagstat
*/

// merge tuples, for when filtered has been run

//ch_bam_filtered_flagstat_for_endorspy.view {it -> "DoubleBefore: $it"}

if (params.run_bam_filtering) {
ch_flagstat_for_endorspy
.join(ch_bam_filtered_flagstat_for_endorspy)
.set{ ch_allflagstats_for_endorspy }

} else {
// Add a file entry to match expected no. tuple elements for endorS.py even if not giving second file
ch_flagstat_for_endorspy
.groupTuple(by: 0)
.map { it -> [it[0], it[1], file('dummy_postfilterflagstat.stats')] }
.set{ ch_allflagstats_for_endorspy }
}

Expand All @@ -1388,9 +1385,16 @@ process endorSpy {

script:
prefix = "${name}"
"""
endorS.py -o json -n ${name} ${stats} ${poststats}
"""

if (params.run_bam_filtering) {
"""
endorS.py -o json -n ${name} ${stats} ${poststats}
"""
} else {
"""
endorS.py -o json -n ${name} ${stats}
"""
}
}


Expand Down Expand Up @@ -1463,7 +1467,7 @@ process markDup{
prefix = "${bam.baseName}"
size = "${params.large_ref}" ? '-c' : ''
"""
picard -Xmx${task.memory.toMega()}M -Xms${task.memory.toMega()}M MarkDuplicates INPUT=$bam OUTPUT=${prefix}._rmdup.bam REMOVE_DUPLICATES=TRUE AS=TRUE METRICS_FILE="${prefix}.rmdup.metrics" VALIDATION_STRINGENCY=SILENT
picard -Xmx${task.memory.toMega()}M -Xms${task.memory.toMega()}M MarkDuplicates INPUT=$bam OUTPUT=${prefix}_rmdup.bam REMOVE_DUPLICATES=TRUE AS=TRUE METRICS_FILE="${prefix}.rmdup.metrics" VALIDATION_STRINGENCY=SILENT
samtools index "${size}" ${prefix}_rmdup.bam
"""
}
Expand Down Expand Up @@ -1830,8 +1834,8 @@ if ( params.gatk_ug_jar != '' ) {
prefix="${bam.baseName}"
skip_coverage = "${params.freebayes_g}" == 0 ? "" : "-g ${params.freebayes_g}"
"""
freebayes -f ${fasta} -p ${params.freebayes_p} -C ${params.freebayes_C} ${skip_coverage} ${bam} > ${bam.baseName}.vcf
pigz -p ${task.cpus} ${bam.baseName}.vcf
freebayes -f ${fasta} -p ${params.freebayes_p} -C ${params.freebayes_C} ${skip_coverage} ${bam} > ${bam.baseName}.freebayes.vcf
pigz -p ${task.cpus} ${bam.baseName}.freebayes.vcf
"""
}

Expand Down
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