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Filter long reads for MALT, bump cpus for FastQC for minigut to pass
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parent
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commit
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4 changed files with 22 additions and 3 deletions
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@ -27,7 +27,7 @@ process {
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// TODO nf-core: Customise requirements for specific processes.
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// TODO nf-core: Customise requirements for specific processes.
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// See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
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// See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
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withLabel:process_low {
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withLabel:process_low {
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cpus = { check_max( 2 * task.attempt, 'cpus' ) }
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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memory = { check_max( 12.GB * task.attempt, 'memory' ) }
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memory = { check_max( 12.GB * task.attempt, 'memory' ) }
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time = { check_max( 4.h * task.attempt, 'time' ) }
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time = { check_max( 4.h * task.attempt, 'time' ) }
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}
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}
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@ -15,7 +15,7 @@ params {
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config_profile_description = 'Minimal test dataset to check pipeline function'
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config_profile_description = 'Minimal test dataset to check pipeline function'
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// Limit resources so that this can run on GitHub Actions
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// Limit resources so that this can run on GitHub Actions
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max_cpus = 2
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max_cpus = 8
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max_memory = '6.GB'
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max_memory = '6.GB'
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max_time = '6.h'
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max_time = '6.h'
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@ -29,3 +29,16 @@ params {
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shortread_clipmerge = true
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shortread_clipmerge = true
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}
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}
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process {
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withName: FASTQC {
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 6.GB * task.attempt, 'memory' ) }
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time = { check_max( 6.h * task.attempt, 'time' ) }
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}
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withName: FASTQC_PROCESSED {
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 6.GB * task.attempt, 'memory' ) }
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time = { check_max( 6.h * task.attempt, 'time' ) }
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}
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}
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@ -14,7 +14,7 @@ workflow DB_CHECK {
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// TODO: make database sheet check
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// TODO: make database sheet check
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// Checks:
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// Checks:
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// 1) no duplicates,
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// 1) no duplicates,
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// 2) dbs with no special arguments does not have quotes, e.g. just `,,` and NOT `,"",`
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// 2) args do not have quotes, e.g. just `,,` and NOT `,"",`
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parsed_samplesheet = DATABASE_CHECK ( dbsheet )
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parsed_samplesheet = DATABASE_CHECK ( dbsheet )
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.csv
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.csv
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.splitCsv ( header:true, sep:',' )
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.splitCsv ( header:true, sep:',' )
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@ -90,9 +90,11 @@ workflow TAXPROFILER {
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MODULE: Run FastQC
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MODULE: Run FastQC
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*/
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*/
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ch_input_for_fastqc = INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore ).dump(tag: "input_to_fastq")
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ch_input_for_fastqc = INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore ).dump(tag: "input_to_fastq")
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FASTQC (
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FASTQC (
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ch_input_for_fastqc
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ch_input_for_fastqc
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)
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)
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ch_versions = ch_versions.mix(FASTQC.out.versions.first())
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ch_versions = ch_versions.mix(FASTQC.out.versions.first())
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CUSTOM_DUMPSOFTWAREVERSIONS (
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CUSTOM_DUMPSOFTWAREVERSIONS (
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@ -137,7 +139,11 @@ workflow TAXPROFILER {
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// We groupTuple to have all samples in one channel for MALT as database
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// We groupTuple to have all samples in one channel for MALT as database
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// loading takes a long time, so we only want to run it once per database
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// loading takes a long time, so we only want to run it once per database
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// TODO document somewhere we only accept illumina short reads for MALT?
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ch_input_for_malt = ch_input_for_profiling.malt
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ch_input_for_malt = ch_input_for_profiling.malt
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.dump(tag: "input_to_malt_prefilter")
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.filter { it[0]['instrument_platform'] == 'ILLUMINA' }
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.dump(tag: "input_to_malt_postfilter")
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.map {
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.map {
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it ->
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it ->
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def temp_meta = [ id: it[2]['db_name']] + it[2]
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def temp_meta = [ id: it[2]['db_name']] + it[2]
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