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67 changes: 4 additions & 63 deletions
67
subworkflows/nf-core/fastq_align_dedup_bismark/tests/nextflow.config
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,74 +1,15 @@ | ||
| params { | ||
| aligner = 'bismark' | ||
| comprehensive = false | ||
| known_splices = null | ||
| unmapped = false | ||
| // Library presets | ||
| pbat = false | ||
| rrbs = false | ||
| slamseq = false | ||
| em_seq = false | ||
| single_cell = false | ||
| accel = false | ||
| cegx = false | ||
| epignome = false | ||
| zymo = false | ||
| // Bismark options | ||
| non_directional = false | ||
| cytosine_report = false | ||
| relax_mismatches = false | ||
| num_mismatches = 0.6 | ||
| // 0.6 will allow a penalty of bp * -0.6 | ||
| // For 100bp reads, this is -60. Mismatches cost -6, gap opening -5 and gap extension -2 | ||
| // So -60 would allow 10 mismatches or ~ 8 x 1-2bp indels | ||
| // Bismark default is 0.2 (L,0,-0.2), Bowtie2 default is 0.6 (L,0,-0.6) | ||
| meth_cutoff = null | ||
| no_overlap = true | ||
| ignore_r1 = 0 | ||
| ignore_r2 = 2 | ||
| ignore_3prime_r1 = 0 | ||
| ignore_3prime_r2 = 2 | ||
| known_splices = null | ||
| local_alignment = false | ||
| minins = null | ||
| maxins = null | ||
| nomeseq = false | ||
|
|
||
| aligner = "bismark" | ||
| cytosine_report = false | ||
| skip_deduplication = false | ||
| } | ||
|
|
||
| process { | ||
| withName: 'BISMARK_ALIGN' { | ||
| ext.args = { [ | ||
| params.aligner == 'bismark_hisat' ? ' --hisat2' : ' --bowtie2', | ||
| params.aligner == 'bismark_hisat' && params.known_splices ? " --known-splicesite-infile <(hisat2_extract_splice_sites.py ${known_splices})" : '', | ||
| params.pbat ? ' --pbat' : '', | ||
| ( params.single_cell || params.non_directional || params.zymo ) ? ' --non_directional' : '', | ||
| params.unmapped ? ' --unmapped' : '', | ||
| params.relax_mismatches ? " --score_min L,0,-${params.num_mismatches}" : '', | ||
| params.local_alignment ? " --local" : '', | ||
| !meta.single_end && params.minins ? " --minins ${params.minins}" : '', | ||
| meta.single_end ? '' : ( | ||
| params.maxins ? " --maxins ${params.maxins}" : ( | ||
| params.em_seq ? " --maxins 1000" : '' | ||
| ) | ||
| ) | ||
| ].join(' ').trim() } | ||
| ext.args = { params.aligner == 'bismark_hisat' ? ' --hisat2' : ' --bowtie2' } | ||
| } | ||
|
|
||
| withName: 'SAMTOOLS_SORT_DEDUPLICATED' { | ||
| ext.prefix = { "${meta.id}.sorted" } | ||
| } | ||
|
|
||
| withName: 'BISMARK_METHYLATIONEXTRACTOR' { | ||
| ext.args = { [ | ||
| params.comprehensive ? ' --comprehensive --merge_non_CpG' : '', | ||
| params.meth_cutoff ? " --cutoff ${params.meth_cutoff}" : '', | ||
| params.nomeseq ? '--CX' : '', | ||
| params.ignore_r1 > 0 ? "--ignore ${params.ignore_r1}" : '', | ||
| params.ignore_3prime_r1 > 0 ? "--ignore_3prime ${params.ignore_3prime_r1}" : '', | ||
| meta.single_end ? '' : (params.no_overlap ? ' --no_overlap' : '--include_overlap'), | ||
| meta.single_end ? '' : (params.ignore_r2 > 0 ? "--ignore_r2 ${params.ignore_r2}" : ""), | ||
| meta.single_end ? '' : (params.ignore_3prime_r2 > 0 ? "--ignore_3prime_r2 ${params.ignore_3prime_r2}": "") | ||
| ].join(' ').trim() } | ||
| } | ||
| } |