Merge pull request #255 from nf-core/config-ordering

Minor clean ups from second release review

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) nf-core community
+Copyright (c) James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, Lauri Mesilaakso, Thomas A. Christensen II, Jianhong Ou, Mahwash Jamy, Maxime Borry, Rafal Stepien, Tanja Normark
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

assets/multiqc_config.yml

@@ -44,11 +44,6 @@ sp:
   fastqc/zip:
     fn: "*_fastqc.zip"
 
-#extra_fn_clean_exts:
-#    - '_fastp'
-#    - '.pe.settings'
-#    - '.se.settings'
-
 top_modules:
   - "fastqc":
       name: "FastQC / Falco (pre-Trimming)"

conf/base.config

@@ -60,6 +60,19 @@ process {
     withName:CUSTOM_DUMPSOFTWAREVERSIONS {
         cache = false
     }
+
+    withName: BRACKEN_BRACKEN {
+        errorStrategy = 'ignore'
+    }
+
+    withName: CENTRIFUGE_KREPORT {
+        errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
+    }
+
+    withName: KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE {
+        errorStrategy = { task.exitStatus in [255,1] ? 'ignore' : 'retry' }
+    }
+
     withName: MEGAN_RMA2INFO_TSV {
         cpus   = { check_max( 1                  , 'cpus'    ) }
         memory = { check_max( 6.GB * task.attempt, 'memory'  ) }

conf/modules.config

@@ -196,8 +196,8 @@ process {
         publishDir = [
             path: { "${params.outdir}/bowtie2/build" },
             mode: params.publish_dir_mode,
-            enabled: params.save_hostremoval_index,
+            pattern: 'bowtie2',
-            pattern: 'bowtie2'
+            enabled: params.save_hostremoval_index
         ]
     }
 
@@ -213,14 +213,14 @@ process {
             [
                 path: { "${params.outdir}/bowtie2/align" },
                 mode: params.publish_dir_mode,
-                enabled: params.save_hostremoval_bam,
+                pattern: '*.bam',
-                pattern: '*.bam'
+                enabled: params.save_hostremoval_bam
             ],
             [
                 path: { "${params.outdir}/bowtie2/align" },
                 mode: params.publish_dir_mode,
-                enabled: params.save_hostremoval_unmapped,
+                pattern: '*.fastq.gz',
-                pattern: '*.fastq.gz'
+                enabled: params.save_hostremoval_unmapped
             ]
         ]
     }
@@ -230,8 +230,8 @@ process {
         publishDir = [
             path: { "${params.outdir}/minimap2/index" },
             mode: params.publish_dir_mode,
-            enabled: params.save_hostremoval_index,
+            pattern: '*.mmi',
-            pattern: '*.mmi'
+            enabled: params.save_hostremoval_index
         ]
     }
 
@@ -240,8 +240,8 @@ process {
         publishDir = [
             path: { "${params.outdir}/minimap2/align" },
             mode: params.publish_dir_mode,
-            enabled: params.save_hostremoval_bam,
+            pattern: '*.bam',
-            pattern: '*.bam'
+            enabled: params.save_hostremoval_bam
         ]
     }
 
@@ -255,8 +255,8 @@ process {
         publishDir = [
             path: { "${params.outdir}/samtools/bam2fq" },
             mode: params.publish_dir_mode,
-            enabled: params.save_hostremoval_unmapped,
+            pattern: '*.fq.gz',
-            pattern: '*.fq.gz'
+            enabled: params.save_hostremoval_unmapped
         ]
     }
 
@@ -354,7 +354,6 @@ process {
     }
 
     withName: BRACKEN_BRACKEN {
-        errorStrategy = 'ignore'
         ext.args = { "${meta.db_params}" }
         ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.bracken" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" }
         publishDir = [
@@ -446,17 +445,16 @@ process {
     }
 
     withName: CENTRIFUGE_CENTRIFUGE {
+        ext.args = { "${meta.db_params}" }
+        ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
         publishDir = [
             path: { "${params.outdir}/centrifuge/${meta.db_name}/" },
             mode: params.publish_dir_mode,
             pattern: '*.{txt,sam,gz}'
         ]
-        ext.args = { "${meta.db_params}" }
-        ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
     }
 
     withName: CENTRIFUGE_KREPORT {
-        errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
         ext.args = { "${meta.db_params}" }
         ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
         publishDir = [
@@ -467,7 +465,6 @@ process {
     }
 
     withName: KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE {
-        errorStrategy = { task.exitStatus in [255,1] ? 'ignore' : 'retry' }
         ext.prefix = { "centrifuge_${meta.id}_combined_reports" }
         publishDir = [
             path: { "${params.outdir}/centrifuge/" },
@@ -477,13 +474,13 @@ process {
     }
 
     withName: KAIJU_KAIJU {
+        ext.args = { "${meta.db_params}" }
         ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.kaiju" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.kaiju" }
         publishDir = [
             path: { "${params.outdir}/kaiju/${meta.db_name}/" },
             mode: params.publish_dir_mode,
             pattern: '*.tsv'
         ]
-        ext.args = { "${meta.db_params}" }
     }
 
     withName: 'KAIJU_KAIJU2TABLE_SINGLE' {

modules/local/kraken2_standard_report.nf

@@ -2,10 +2,10 @@ process KRAKEN2_STANDARD_REPORT {
     tag "$meta.id"
     label 'process_single'
 
-    conda "conda-forge::sed=4.8"
+    conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' :
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'biocontainers/biocontainers:v1.2.0_cv2' }"
+        'ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(report)

modules/local/krona_cleanup.nf

@@ -4,8 +4,8 @@ process KRONA_CLEANUP {
 
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'biocontainers/biocontainers:v1.2.0_cv1' }"
+        'ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(krona, stageAs: 'uncleaned.krona.txt')

nextflow.config

@@ -300,7 +300,7 @@ dag {
 
 manifest {
     name            = 'nf-core/taxprofiler'
-    author          = """nf-core community"""
+    author          = """James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, Lauri Mesilaakso, Thomas A. Christensen II, Jianhong Ou, Mahwash Jamy, Maxime Borry, Rafal Stepien, Tanja Normark"""
     homePage        = 'https://github.com/nf-core/taxprofiler'
     description     = """Taxonomic classification and profiling of shotgun metagenomic data"""
     mainScript      = 'main.nf'

subworkflows/local/db_check.nf

@@ -63,8 +63,8 @@ def validate_db_rows(LinkedHashMap row){
         def expected_headers = ['tool', 'db_name', 'db_params', 'db_path']
         if ( !row.keySet().containsAll(expected_headers) ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database input sheet - malformed column names. Please check input TSV. Column names should be: ${expected_keys.join(", ")}"
 
-        // valid tools specified// TIFNISIH LIST
+        // valid tools specified
-        def expected_tools = [ "bracken", "centrifuge", "diamond", "kaiju",  "kraken2", "krakenuniq", "malt", "metaphlan3", "motus" ]
+        def expected_tools = [ "bracken", "centrifuge", "diamond", "kaiju", "kraken2", "krakenuniq", "malt", "metaphlan3", "motus" ]
         if ( !expected_tools.contains(row.tool) ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid tool name. Please see documentation for all supported profilers. Error in: ${row}"
 
         // detect quotes in params