mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-13 05:53:09 +00:00
Add taxpasta_merge to taxprofiler
This commit is contained in:
parent
21d9135b14
commit
de6a4214ef
8 changed files with 302 additions and 47 deletions
|
@ -533,6 +533,21 @@ process {
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]
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}
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withName: TAXPASTA_MERGE {
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ext.args = {
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[
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"-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.taxpasta_standardisation_format}",
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params.taxpasta_add_taxonomy ? "-p" : "",
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params.taxpasta_add_samplesheet ? "-s" :""
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].join(',').replaceAll(','," ")
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}
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publishDir = [
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path: { "${params.outdir}/taxpasta/" },
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mode: params.publish_dir_mode,
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pattern: '*.{tsv,csv,arrow,parquet,biom}'
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]
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}
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withName: CUSTOM_DUMPSOFTWAREVERSIONS {
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publishDir = [
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path: { "${params.outdir}/pipeline_info" },
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@ -25,7 +25,7 @@ params {
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perform_shortread_qc = true
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perform_longread_qc = true
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shortread_qc_mergepairs = true
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perform_shortread_complexityfilter = true
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perform_shortread_complexityfilter = false
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perform_shortread_hostremoval = true
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perform_longread_hostremoval = true
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perform_runmerging = true
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@ -44,7 +44,7 @@ params {
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malt_save_reads = true
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kraken2_save_reads = true
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centrifuge_save_reads = true
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diamond_save_reads = true
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run_profile_standardisation = true
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}
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process {
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173
modules.json
173
modules.json
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@ -8,212 +8,301 @@
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"adapterremoval": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"bbmap/bbduk": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"bowtie2/align": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"bowtie2/build": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"bracken/bracken": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"bracken/combinebrackenoutputs": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"cat/fastq": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"centrifuge/centrifuge": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"centrifuge/kreport": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"custom/dumpsoftwareversions": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"diamond/blastx": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"falco": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"],
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"installed_by": [
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"modules"
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],
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"patch": "modules/nf-core/falco/falco.diff"
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},
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"fastp": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"fastqc": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"filtlong": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"gunzip": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"kaiju/kaiju": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"kaiju/kaiju2krona": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"kaiju/kaiju2table": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"kraken2/kraken2": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"krakentools/combinekreports": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"krakentools/kreport2krona": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"krakenuniq/preloadedkrakenuniq": {
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"branch": "master",
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"git_sha": "a6eb17f65b3ee5761c25c075a6166c9f76733cee",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"krona/ktimporttaxonomy": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"krona/ktimporttext": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"malt/run": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"megan/rma2info": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"metaphlan3/mergemetaphlantables": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"metaphlan3/metaphlan3": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"minimap2/align": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"minimap2/index": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"motus/merge": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"motus/profile": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"porechop/porechop": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"],
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"installed_by": [
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"modules"
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],
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"patch": "modules/nf-core/porechop/porechop/porechop-porechop.diff"
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},
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"prinseqplusplus": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"samtools/bam2fq": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"samtools/index": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"samtools/stats": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"samtools/view": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"taxpasta/merge": {
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"branch": "master",
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"git_sha": "74ab450ed05e034d049c00f6e2853de2c31594b4",
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"installed_by": [
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"modules"
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]
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},
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"untar": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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}
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}
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}
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}
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}
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}
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}
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47
modules/nf-core/taxpasta/merge/main.nf
generated
Normal file
47
modules/nf-core/taxpasta/merge/main.nf
generated
Normal file
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@ -0,0 +1,47 @@
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process TAXPASTA_MERGE {
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tag "$meta.id"
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label 'process_single'
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conda "bioconda::taxpasta=0.1.1"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/taxpasta:0.1.1--pyhdfd78af_0':
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'quay.io/biocontainers/taxpasta:0.1.1--pyhdfd78af_0' }"
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input:
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tuple val(meta), path(profiles)
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path taxonomy
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path samplesheet
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output:
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tuple val(meta), path("*.{tsv,csv,arrow,parquet,biom}"), emit: merged_profiles
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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// N.B.: Taxpasta requires a --profiler option and will fail without it.
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// This must be specified via a `nextflow.config` or `modules.config`, for
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// example, as "--profiler kraken2". Additionally, it requires a --output
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// option with the output file name. The desired format will be parsed from
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// the name and should correspond to the output pattern specified above,
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// e.g., "--output ${task.ext.prefix}.tsv".
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def taxonomy_option = taxonomy ? "--taxonomy ${taxonomy}" : ''
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def samplesheet_input = samplesheet ? "-s ${samplesheet}" : ''
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"""
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taxpasta merge \\
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$args \\
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$taxonomy_option \\
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$samplesheet_input \\
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$profiles
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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taxpasta: \$(taxpasta --version)
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END_VERSIONS
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"""
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}
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58
modules/nf-core/taxpasta/merge/meta.yml
generated
Normal file
58
modules/nf-core/taxpasta/merge/meta.yml
generated
Normal file
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@ -0,0 +1,58 @@
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name: "taxpasta_merge"
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description: Standardise and merge two or more taxonomic profiles into a single table
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keywords:
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- taxonomic profile
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- standardise
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- standardisation
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- metagenomics
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- taxonomic profiling
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- otu tables
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- taxon tables
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tools:
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- "taxpasta":
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description: "TAXonomic Profile Aggregation and STAndardisation"
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homepage: "https://taxpasta.readthedocs.io/"
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documentation: "https://taxpasta.readthedocs.io/"
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tool_dev_url: "https://github.com/taxprofiler/taxpasta"
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doi: ""
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licence: "['Apache-2.0']"
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input:
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- meta:
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type: map
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description: |
|
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- profiles:
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type: file
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description: A list of taxonomic profiler output files (typically in text format, mandatory)
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pattern: "*.{tsv,csv,arrow,parquet,biom}"
|
||||
- samplesheet:
|
||||
type: file
|
||||
description:
|
||||
A samplesheet describing the sample name and a filepath to a taxonomic abundance profile that needs to be relative
|
||||
from the work environment. The profiles must be provided even if you give a samplesheet as argument (optional)
|
||||
pattern: "*.{tsv,csv,ods,xlsx,arrow,parquet}"
|
||||
- taxonomy:
|
||||
type: directory
|
||||
description: Directory containing at a minimum nodes.dmp and names.dmp files (optional)
|
||||
pattern: "*/"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- merged_profiles:
|
||||
type: file
|
||||
description: Output file with standardised multiple profiles in one go and have all profiles combined into a single table.
|
||||
pattern: "*.{tsv,csv,ods,xlsx,arrow,parquet,biom}"
|
||||
|
||||
authors:
|
||||
- "@sofstam"
|
||||
- "@jfy133"
|
|
@ -155,8 +155,11 @@ params {
|
|||
krona_taxonomy_directory = null
|
||||
|
||||
// profile standardisation
|
||||
run_profile_standardisation = false
|
||||
generate_biom_output = false
|
||||
run_profile_standardisation = false
|
||||
taxpasta_add_taxonomy = false
|
||||
taxpasta_add_samplesheet = false
|
||||
taxpasta_standardisation_format = 'tsv'
|
||||
generate_biom_output = false
|
||||
}
|
||||
|
||||
// Load base.config by default for all pipelines
|
||||
|
@ -242,6 +245,15 @@ profiles {
|
|||
executor.cpus = 16
|
||||
executor.memory = 60.GB
|
||||
}
|
||||
hasta {
|
||||
includeConfig 'conf/hasta.config'
|
||||
}
|
||||
dev_priority {
|
||||
params {
|
||||
priority = 'development'
|
||||
clusterOptions = "--qos=low"
|
||||
}
|
||||
}
|
||||
test { includeConfig 'conf/test.config' }
|
||||
test_full { includeConfig 'conf/test_full.config' }
|
||||
test_noprofiling { includeConfig 'conf/test_noprofiling.config' }
|
||||
|
|
|
@ -767,5 +767,19 @@
|
|||
{
|
||||
"$ref": "#/definitions/reference_genome_options"
|
||||
}
|
||||
]
|
||||
],
|
||||
"properties": {
|
||||
"add_taxonomy": {
|
||||
"type": "string",
|
||||
"default": "false"
|
||||
},
|
||||
"add_samplesheet": {
|
||||
"type": "string",
|
||||
"default": "false"
|
||||
},
|
||||
"standardisation_taxpasta_format": {
|
||||
"type": "string",
|
||||
"default": "tsv"
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
@ -8,6 +8,7 @@ include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_KRAKEN
|
|||
include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE } from '../../modules/nf-core/krakentools/combinekreports/main'
|
||||
include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../modules/nf-core/metaphlan3/mergemetaphlantables/main'
|
||||
include { MOTUS_MERGE } from '../../modules/nf-core/motus/merge/main'
|
||||
include { TAXPASTA_MERGE } from '../../modules/nf-core/taxpasta/merge/main'
|
||||
|
||||
workflow STANDARDISATION_PROFILES {
|
||||
take:
|
||||
|
@ -21,6 +22,20 @@ workflow STANDARDISATION_PROFILES {
|
|||
ch_versions = Channel.empty()
|
||||
ch_multiqc_files = Channel.empty()
|
||||
|
||||
//Taxpasta standardisation
|
||||
ch_input_for_taxpasta = profiles
|
||||
.map {
|
||||
meta, profile ->
|
||||
def meta_new = [:]
|
||||
meta_new.id = meta.db_name
|
||||
meta_new.tool = meta.tool == 'metaphlan3' ? 'metaphlan' : meta.tool == 'malt' ? 'megan6' : meta.tool
|
||||
[meta_new, profile]
|
||||
}
|
||||
.groupTuple ()
|
||||
|
||||
TAXPASTA_MERGE (ch_input_for_taxpasta, [], [])
|
||||
|
||||
|
||||
/*
|
||||
Split profile results based on tool they come from
|
||||
*/
|
||||
|
@ -74,6 +89,8 @@ workflow STANDARDISATION_PROFILES {
|
|||
[[id:it[0]], it[1]]
|
||||
}
|
||||
|
||||
|
||||
|
||||
KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE ( ch_profiles_for_centrifuge )
|
||||
ch_standardised_tables = ch_standardised_tables.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.txt )
|
||||
ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.txt )
|
||||
|
@ -125,6 +142,8 @@ workflow STANDARDISATION_PROFILES {
|
|||
ch_multiqc_files = ch_multiqc_files.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.txt )
|
||||
ch_versions = ch_versions.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.versions )
|
||||
|
||||
ch_standardised_tables.dump (tag: 'standardised')
|
||||
|
||||
// mOTUs
|
||||
|
||||
// mOTUs has a 'single' database, and cannot create custom ones.
|
||||
|
@ -149,6 +168,7 @@ workflow STANDARDISATION_PROFILES {
|
|||
|
||||
emit:
|
||||
tables = ch_standardised_tables
|
||||
taxpasta = TAXPASTA_MERGE.out.merged_profiles
|
||||
versions = ch_versions
|
||||
mqc = ch_multiqc_files
|
||||
}
|
||||
|
|
Loading…
Reference in a new issue