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update msa_alignment subworkflow to not use conditional includes
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,35 +1,57 @@ | ||
| if ( params.aligner == "clustalo/align" ) { | ||
| include { CLUSTALO_ALIGN as ALIGNER } from '../../../modules/mirpedrol/clustalo/align/main' | ||
| } else if ( params.aligner == "famsa/align" ) { | ||
| include { FAMSA_ALIGN as ALIGNER } from '../../../modules/mirpedrol/famsa/align/main' | ||
| } else if ( params.aligner == "kalign/align" ) { | ||
| include { KALIGN_ALIGN as ALIGNER } from '../../../modules/mirpedrol/kalign/align/main' | ||
| } else if ( params.aligner == "learnmsa/align" ) { | ||
| include { LEARNMSA_ALIGN as ALIGNER } from '../../../modules/mirpedrol/learnmsa/align/main' | ||
| } else if ( params.aligner == "mafft" ) { | ||
| include { MAFFT as ALIGNER } from '../../../modules/mirpedrol/mafft/main' | ||
| } else if ( params.aligner == "magus/align" ) { | ||
| include { MAGUS_ALIGN as ALIGNER } from '../../../modules/mirpedrol/magus/align/main' | ||
| } else if ( params.aligner == "muscle5/super5" ) { | ||
| include { MUSCLE5_SUPER5 as ALIGNER } from '../../../modules/mirpedrol/muscle5/super5/main' | ||
| } else if ( params.aligner == "tcoffee/align" ) { | ||
| include { TCOFFEE_ALIGN as ALIGNER } from '../../../modules/mirpedrol/tcoffee/align/main' | ||
| } | ||
| include { CLUSTALO_ALIGN } from '../../../modules/mirpedrol/clustalo/align/main' | ||
| include { FAMSA_ALIGN } from '../../../modules/mirpedrol/famsa/align/main' | ||
| include { KALIGN_ALIGN } from '../../../modules/mirpedrol/kalign/align/main' | ||
| include { LEARNMSA_ALIGN } from '../../../modules/mirpedrol/learnmsa/align/main' | ||
| include { MAFFT } from '../../../modules/mirpedrol/mafft/main' | ||
| include { MAGUS_ALIGN } from '../../../modules/mirpedrol/magus/align/main' | ||
| include { MUSCLE5_SUPER5 } from '../../../modules/mirpedrol/muscle5/super5/main' | ||
| include { TCOFFEE_ALIGN } from '../../../modules/mirpedrol/tcoffee/align/main' | ||
|
|
||
| workflow MSA_ALIGNMENT { | ||
|
|
||
| take: | ||
| ch_fasta // channel: [ meta, fasta ] | ||
|
|
||
| main: | ||
| def ch_out_alignment = Channel.empty() | ||
| def ch_versions = Channel.empty() | ||
|
|
||
| ch_versions = Channel.empty() | ||
|
|
||
| ALIGNER ( ch_fasta ) | ||
| ch_versions = ch_versions.mix(ALIGNER.out.versions.first()) | ||
| if ( params.aligner == "clustalo/align" ) { | ||
| CLUSTALO_ALIGN( ch_fasta ) | ||
| ch_out_alignment = ch_out_alignment.mix(CLUSTALO_ALIGN.out.alignment) | ||
| ch_versions = ch_versions.mix(CLUSTALO_ALIGN.out.versions.first()) | ||
| } else if ( params.aligner == "famsa/align" ) { | ||
| FAMSA_ALIGN( ch_fasta ) | ||
| ch_out_alignment = ch_out_alignment.mix(FAMSA_ALIGN.out.alignment) | ||
| ch_versions = ch_versions.mix(FAMSA_ALIGN.out.versions.first()) | ||
| } else if ( params.aligner == "kalign/align" ) { | ||
| KALIGN_ALIGN( ch_fasta ) | ||
| ch_out_alignment = ch_out_alignment.mix(KALIGN_ALIGN.out.alignment) | ||
| ch_versions = ch_versions.mix(KALIGN_ALIGN.out.versions.first()) | ||
| } else if ( params.aligner == "learnmsa/align" ) { | ||
| LEARNMSA_ALIGN( ch_fasta ) | ||
| ch_out_alignment = ch_out_alignment.mix(LEARNMSA_ALIGN.out.alignment) | ||
| ch_versions = ch_versions.mix(LEARNMSA_ALIGN.out.versions.first()) | ||
| } else if ( params.aligner == "mafft" ) { | ||
| MAFFT( ch_fasta ) | ||
| ch_out_alignment = ch_out_alignment.mix(MAFFT.out.alignment) | ||
| ch_versions = ch_versions.mix(MAFFT.out.versions.first()) | ||
| } else if ( params.aligner == "magus/align" ) { | ||
| MAGUS_ALIGN( ch_fasta ) | ||
| ch_out_alignment = ch_out_alignment.mix(MAGUS_ALIGN.out.alignment) | ||
| ch_versions = ch_versions.mix(MAGUS_ALIGN.out.versions.first()) | ||
| } else if ( params.aligner == "muscle5/super5" ) { | ||
| MUSCLE5_SUPER5( ch_fasta ) | ||
| ch_out_alignment = ch_out_alignment.mix(MUSCLE5_SUPER5.out.alignment) | ||
| ch_versions = ch_versions.mix(MUSCLE5_SUPER5.out.versions.first()) | ||
| } else if ( params.aligner == "tcoffee/align" ) { | ||
| TCOFFEE_ALIGN( ch_fasta ) | ||
| ch_out_alignment = ch_out_alignment.mix(TCOFFEE_ALIGN.out.alignment) | ||
| ch_versions = ch_versions.mix(TCOFFEE_ALIGN.out.versions.first()) | ||
| } | ||
|
|
||
| emit: | ||
| alignment = ALIGNER.out.alignment // channel: [ meta, *.aln.gz ] | ||
| versions = ch_versions // channel: [ versions.yml ] | ||
| alignment = ch_out_alignment // channel: [ meta, *.aln.gz ] | ||
| versions = ch_versions // channel: [ versions.yml ] | ||
| } | ||
|
|