61 lines
2.4 KiB
Plaintext
61 lines
2.4 KiB
Plaintext
process map_reads{
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/*
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Map reads to reference using minimap2.
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Filter reads by mapping quality.
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Filter internally-primed reads.
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*/
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label "isoforms"
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cpus params.threads
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memory "31 GB"
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publishDir path: "${params.out_dir}/${publish_prefix_bams}", mode: 'copy', pattern: "${sample_id}_reads_aln_sorted.bam*", overwrite: true
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input:
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tuple val(sample_id), path (fastq_reads), path(index), path(reference)
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val publish_prefix_bams
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output:
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tuple val(sample_id),
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path("${sample_id}_reads_aln_sorted.bam"),
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path("${sample_id}_reads_aln_sorted.bam.bai"),
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emit: bam
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tuple val(sample_id), path("${sample_id}_read_aln_stats.tsv"), emit: stats
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script:
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def ContextFilter = """AlnContext: { Ref: "${reference}", LeftShift: -${params.poly_context},
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RightShift: ${params.poly_context}, RegexEnd: "[Aa]{${params.max_poly_run},}",
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Stranded: True,Invert: True, Tsv: "internal_priming_fail.tsv"} """
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def mm2_threads = Math.max(task.cpus - 3, 1)
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"""
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minimap2 -t ${mm2_threads} -ax splice ${params.minimap2_opts} ${index} ${fastq_reads}\
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| samtools view -q ${params.minimum_mapping_quality} -F 2304 -Sb -\
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| seqkit bam -j 1 -x -T '${ContextFilter}' -\
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| samtools sort --write-index -@ 1 -o "${sample_id}_reads_aln_sorted.bam##idx##${sample_id}_reads_aln_sorted.bam.bai" - ;
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((cat "${sample_id}_reads_aln_sorted.bam" | seqkit bam -s -j 1 - 2>&1) | tee "${sample_id}_read_aln_stats.tsv" ) || true
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# Add sample id header and column; remove last column (File)
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cat "${sample_id}_read_aln_stats.tsv" \
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| sed "s/^/${sample_id} /" \
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| sed "1 s/^${sample_id}/sample_id/" \
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| awk 'NF{NF-=1};1' \
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> tmp
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mv tmp "${sample_id}_read_aln_stats.tsv"
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if [[ -s "internal_priming_fail.tsv" ]];
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then
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tail -n +2 "internal_priming_fail.tsv" | awk '{print ">" \$1 "\\n" \$4 }' - > "context_internal_priming_fail_start.fasta"
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tail -n +2 "internal_priming_fail.tsv" | awk '{print ">" \$1 "\\n" \$6 }' - > "context_internal_priming_fail_end.fasta"
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fi
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"""
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}
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workflow reference_assembly {
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take:
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index
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reference
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fastq_reads
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publish_prefix_bams
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main:
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map_reads(fastq_reads.combine(index).combine(reference), publish_prefix_bams)
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emit:
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bam = map_reads.out.bam
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stats = map_reads.out.stats
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}
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