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Fix MALT save_alignemnts reads and some clean up

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James Fellows Yates 2022-06-03 22:29:04 +02:00
parent d48b3be5a7
commit 9462032d00
4 changed files with 9 additions and 8 deletions
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3
conf/test.config
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@ -47,4 +47,7 @@ process {
withName: MALT_RUN { withName: MALT_RUN {
maxForks = 1 maxForks = 1
} }
withName: MEGAN_RMA2INFO {
maxForks = 1
}
} }

2
nextflow.config
View file

@ -196,7 +196,7 @@ profiles {
test { includeConfig 'conf/test.config' } test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' } test_full { includeConfig 'conf/test_full.config' }
test_noprofiling { includeConfig 'conf/test_noprofiling.config' } test_noprofiling { includeConfig 'conf/test_noprofiling.config' }
test_nopreprocessing { includeConfig 'conf/test_preprocessing.config' } test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' }
} }
// Load igenomes.config if required // Load igenomes.config if required

2
subworkflows/local/longread_preprocessing.nf
View file

@ -48,7 +48,7 @@ workflow LONGREAD_PREPROCESSING {
} }
FASTQC_PROCESSED ( ch_processed_reads.dump(tag: "filtlong") ) FASTQC_PROCESSED ( ch_processed_reads )
ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip ) ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip )
emit: emit:

10
subworkflows/local/profiling.nf
View file

@ -66,19 +66,17 @@ workflow PROFILING {
.filter { it[0]['instrument_platform'] == 'ILLUMINA' } .filter { it[0]['instrument_platform'] == 'ILLUMINA' }
.map { .map {
meta, reads, db_meta, db -> meta, reads, db_meta, db ->
def sam_format = params.malt_save_reads ? ' --alignments' : "" def sam_format = params.malt_save_reads ? ' --alignments ./ -za false' : ""
// TODO No MALT SAM?
// TODO check all aligned reads published
// TODO try turning on/off aligned reads
// TODO wut? [9a/a441d6] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MALT_RUN (null) // TODO wut? [9a/a441d6] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MALT_RUN (null)
def temp_meta = [ id: meta['db_name'] ] def temp_meta = [ id: meta['db_name'] ]
def new_db_meta = db_meta.clone() def new_db_meta = db_meta.clone()
new_db_meta['db_params'] = db_meta['db_params'] + sam_format new_db_meta['db_params'] = db_meta['db_params'] + sam_format
def new_meta = temp_meta + new_db_meta def new_meta = temp_meta + new_db_meta
new_meta['id'] = new_meta['db_name']
[ new_meta, reads, db ] [ new_meta, reads, db ]
} }
.groupTuple(by: [0,2]) .groupTuple(by: [0,2])
.dump(tag: "into_malt")
.multiMap { .multiMap {
it -> it ->
reads: [ it[0], it[1].flatten() ] reads: [ it[0], it[1].flatten() ]
@ -192,7 +190,7 @@ workflow PROFILING {
// this will replace output file! // this will replace output file!
ch_diamond_reads_format = params.diamond_save_reads ? 'sam' : params.diamond_output_format ch_diamond_reads_format = params.diamond_save_reads ? 'sam' : params.diamond_output_format
DIAMOND_BLASTX ( ch_input_for_diamond.reads, ch_input_for_diamond.db, params.diamond_output_format, [] ) DIAMOND_BLASTX ( ch_input_for_diamond.reads, ch_input_for_diamond.db, ch_diamond_reads_format , [] )
ch_versions = ch_versions.mix( DIAMOND_BLASTX.out.versions.first() ) ch_versions = ch_versions.mix( DIAMOND_BLASTX.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( DIAMOND_BLASTX.out.tsv ) ch_raw_profiles = ch_raw_profiles.mix( DIAMOND_BLASTX.out.tsv )