Merge pull request #37 from CFIA-NCFAD/dev

Release 3.3.1
peterk87 · Aug 2, 2023 · 34c23be · 34c23be
2 parents b0d6575 + 2ccb2b4
commit 34c23be
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -31,7 +31,7 @@ jobs:
  strategy:
  matrix:
  # Nextflow versions: check pipeline minimum and current latest
- nxf_ver: ['21.10.6', '23.04.1']
+ nxf_ver: ['22.10.1', '23.04.1']
  steps:
  - name: Check out pipeline code
  uses: actions/checkout@v2
@@ -111,7 +111,7 @@ jobs:
  strategy:
  matrix:
  # Nextflow versions: check pipeline minimum and current latest
- nxf_ver: ['21.10.6', '23.04.1']
+ nxf_ver: ['22.10.1', '23.04.1']
  steps:
  - name: Check out pipeline code
  uses: actions/checkout@v2

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,12 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[3.3.1](https://github.com/CFIA-NCFAD/nf-flu/releases/tag/3.3.1)] - 2023-08-02
+
+### Fixes
+
+* Conda/Mamba env creation when using `conda`/`mamba` profile (#35)
+
 ## [[3.3.0](https://github.com/CFIA-NCFAD/nf-flu/releases/tag/3.3.0)] - 2023-07-11
 
 This release migrates to more recently updated Influenza virus sequences since the last update for the [NCBI Influenza DB FTP data](https://ftp.ncbi.nih.gov/genomes/INFLUENZA/) was in 2020-10-13. By default, all Orthomyxoviridae virus sequences were parsed from the daily updated NCBI Viruses [`AllNucleotide.fa`](https://ftp.ncbi.nlm.nih.gov/genomes/Viruses/AllNucleotide/) and [`AllNuclMetadata.csv.gz`](https://ftp.ncbi.nlm.nih.gov/genomes/Viruses/AllNuclMetadata/AllNuclMetadata.csv.gz) and uploaded to [Figshare](https://figshare.com/articles/dataset/2023-06-14_-_NCBI_Viruses_-_Orthomyxoviridae/23608782) as Zstd compressed files. nf-flu no longer uses the [influenza.fna.gz](https://ftp.ncbi.nih.gov/genomes/INFLUENZA/influenza.fna.gz) and [genomeset.dat.gz](https://ftp.ncbi.nih.gov/genomes/INFLUENZA/genomeset.dat.gz) files for Influenza sequences and metadata, respectively.

diff --git a/conf/modules_illumina.config b/conf/modules_illumina.config
@@ -1,5 +1,16 @@
 // Illumina subworkflow process configuration
 process {
+ withName: 'CHECK_SAMPLE_SHEET' {
+ ext.args = ''
+ publishDir = [
+ [
+ path: { "${params.tracedir}/" },
+ mode: params.publish_dir_mode,
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+ ]
+ ]
+ }
+
  withName: 'IRMA' {
  publishDir = [
  [

diff --git a/conf/modules_nanopore.config b/conf/modules_nanopore.config
@@ -1,5 +1,16 @@
 // Nanopore subworkflow process configuration
 process {
+ withName: 'CHECK_SAMPLE_SHEET' {
+ ext.args = ''
+ publishDir = [
+ [
+ path: { "${params.tracedir}/" },
+ mode: params.publish_dir_mode,
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+ ]
+ ]
+ }
+
  withName: 'IRMA' {
  publishDir = [
  [

diff --git a/docs/usage.md b/docs/usage.md
@@ -311,20 +311,6 @@ Do not use coloured log outputs.
 
 Directory to keep pipeline Nextflow logs and reports.
 
-#### `--enable_conda`
-
-- Optional
-- Type: boolean
-
-Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.
-
-#### `--use_mamba`
-
-- Optional
-- Type: boolean
-
-Use Mamba in place of Conda for faster Conda env creation.
-
 #### `--singularity_pull_docker_container`
 
 - Optional

diff --git a/modules.json b/modules.json
@@ -5,12 +5,6 @@
  "nf-core/modules": {
  "custom/dumpsoftwareversions": {
  "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
- },
- "multiqc": {
- "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"
- },
- "prokka": {
- "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
  }
  }
  }

diff --git a/modules/local/bcftools.nf b/modules/local/bcftools.nf
@@ -5,7 +5,7 @@ process BCF_CONSENSUS {
  tag "$sample|$segment|$ref_id"
  label 'process_medium'
 
- conda (params.enable_conda ? 'bioconda::bcftools=1.15.1 conda-forge::gsl=2.7' : null)
+ conda 'bioconda::bcftools=1.15.1 conda-forge::gsl=2.7'
  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
  container 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0'
  } else {
@@ -49,7 +49,7 @@ process BCF_FILTER {
  tag "$sample|$segment|$ref_id"
  label 'process_low'
 
- conda (params.enable_conda ? 'bioconda::bcftools=1.15.1 conda-forge::gsl=2.7' : null)
+ conda 'bioconda::bcftools=1.15.1 conda-forge::gsl=2.7'
  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
  container 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0'
  } else {
@@ -94,7 +94,7 @@ process BCFTOOLS_STATS {
  tag "$sample|$segment|$ref_id"
  label 'process_low'
 
- conda (params.enable_conda ? 'bioconda::bcftools=1.15.1 conda-forge::gsl=2.7' : null)
+ conda 'bioconda::bcftools=1.15.1 conda-forge::gsl=2.7'
  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
  container 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0'
  } else {

diff --git a/modules/local/blast_makeblastdb.nf b/modules/local/blast_makeblastdb.nf
@@ -3,7 +3,7 @@ process BLAST_MAKEBLASTDB {
  tag "$fasta"
  label 'process_low'
 
- conda (params.enable_conda ? 'bioconda::blast=2.14.0' : null)
+ conda 'bioconda::blast=2.14.0'
  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
  container 'https://depot.galaxyproject.org/singularity/blast:2.14.0--h7d5a4b4_1'
  } else {

diff --git a/modules/local/blastn.nf b/modules/local/blastn.nf
@@ -2,7 +2,7 @@ process BLAST_BLASTN {
  tag "$meta.id"
  label 'process_high'
 
- conda (params.enable_conda ? 'bioconda::blast=2.14.0' : null)
+ conda 'bioconda::blast=2.14.0'
  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
  container 'https://depot.galaxyproject.org/singularity/blast:2.14.0--h7d5a4b4_1'
  } else {

diff --git a/modules/local/blastn_report.nf b/modules/local/blastn_report.nf
@@ -1,18 +1,12 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
 process BLASTN_REPORT {
- tag "$meta.id"
- label 'process_low'
- conda (params.enable_conda ? 'conda-forge::python=3.9 conda-forge::biopython=1.78 conda-forge::openpyxl=3.0.7 conda-forge::pandas=1.2.4 conda-forge::rich=10.2.2 conda-forge::typer=0.3.2 conda-forge::xlsxwriter=1.4.3' : null)
-  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-  container 'https://depot.galaxyproject.org/singularity/mulled-v2-693e24f156d01a5f55647120be99929b01b30949:609c862c3470382215fc1b2d9d8a4e9637b2e25f-0'
-  } else {
-  container 'quay.io/biocontainers/mulled-v2-693e24f156d01a5f55647120be99929b01b30949:609c862c3470382215fc1b2d9d8a4e9637b2e25f-0'
-  }
+  tag "$meta.id"
+  label 'process_low'
+  conda 'conda-forge::python=3.9 conda-forge::biopython=1.78 conda-forge::openpyxl=3.0.7 conda-forge::pandas=1.2.4 conda-forge::rich=10.2.2 conda-forge::typer=0.3.2 conda-forge::xlsxwriter=1.4.3'
+ if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+ container 'https://depot.galaxyproject.org/singularity/mulled-v2-693e24f156d01a5f55647120be99929b01b30949:609c862c3470382215fc1b2d9d8a4e9637b2e25f-0'
+ } else {
+ container 'quay.io/biocontainers/mulled-v2-693e24f156d01a5f55647120be99929b01b30949:609c862c3470382215fc1b2d9d8a4e9637b2e25f-0'
+ }
 
  input:
  tuple val(meta), path(blastn_results)
@@ -25,10 +19,12 @@ process BLASTN_REPORT {
  script:
  """
  get_blastn_report.py \\
- -b $blastn_results \\
- --min-aln-length ${params.min_aln_length} \\
- -x ${meta.id}-blastn-report.xlsx
+ -b $blastn_results \\
+ --min-aln-length ${params.min_aln_length} \\
+ -x ${meta.id}-blastn-report.xlsx
+
  ln -s .command.log get_blastn_report.log
+
  cat <<-END_VERSIONS > versions.yml
  "${task.process}":
  python: \$(python --version | sed 's/Python //g')

diff --git a/modules/local/cat_illumina_fastq.nf b/modules/local/cat_illumina_fastq.nf
@@ -5,7 +5,7 @@ process CAT_ILLUMINA_FASTQ {
  tag "$meta.id"
  label 'process_single'
 
- conda (params.enable_conda ? "conda-forge::perl" : null)
+ conda "conda-forge::perl"
  // use BLAST container here since it has Perl and is required by other
  // processes in the pipeline
  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

diff --git a/modules/local/check_ref_fasta.nf b/modules/local/check_ref_fasta.nf
@@ -1,6 +1,6 @@
 process CHECK_REF_FASTA {
  tag "$fasta"
- conda (params.enable_conda ? 'bioconda::shiptv=0.4.0' : null)
+ conda 'bioconda::shiptv=0.4.0'
  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
  container 'https://depot.galaxyproject.org/singularity/shiptv:0.4.0--pyh5e36f6f_0'
  } else {

diff --git a/modules/local/check_sample_sheet.nf b/modules/local/check_sample_sheet.nf
@@ -1,8 +1,6 @@
 process CHECK_SAMPLE_SHEET {
- publishDir "${params.tracedir}/",
- mode: params.publish_dir_mode
  // using shiptv container since it has pandas, rich, typer installed
- conda (params.enable_conda ? 'bioconda::shiptv=0.4.0' : null)
+ conda 'bioconda::shiptv=0.4.0'
  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
  container 'https://depot.galaxyproject.org/singularity/shiptv:0.4.0--pyh5e36f6f_0'
  } else {

diff --git a/modules/local/clair3.nf b/modules/local/clair3.nf
@@ -5,7 +5,7 @@ process CLAIR3 {
  tag "$sample|$segment|$ref_id"
  label 'process_low'
 
- conda (params.enable_conda ? 'bioconda::clair3==1.0.2' : null)
+ conda 'bioconda::clair3==1.0.2'
  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
  container 'https://depot.galaxyproject.org/singularity/clair3:1.0.2--py39hb9dc472_0'
  } else {
@@ -30,14 +30,15 @@ process CLAIR3 {
  clair3_dir = "${prefix}.clair3"
  clair3_log = "${clair3_dir}/run_clair3.log"
  model_suffix = "models/${params.clair3_variant_model}"
+ using_conda = (workflow.containerEngine == null || workflow.containerEngine == '')
  """
  CLAIR_BIN_DIR=\$(dirname \$(which run_clair3.sh))
  if [[ "${params.clair3_user_variant_model}" != "" ]] ; then
  MODEL_PATH=${model_path}
  else
- if [[ ${params.enable_conda} = true ]] ; then
+ if [[ ${using_conda} = true ]] ; then
  MODEL_PATH="\$CLAIR_BIN_DIR/${model_suffix}"
- else [[ ${params.enable_conda} = false ]]
+ else [[ ${using_conda} = false ]]
  MODEL_PATH="/usr/local/bin/models/${params.clair3_variant_model}"
  fi
  fi

diff --git a/modules/local/coverage_plot.nf b/modules/local/coverage_plot.nf
@@ -4,7 +4,7 @@ process COVERAGE_PLOT{
  tag "$sample|$segment|$ref_id"
  label 'process_low'
 
- conda (params.enable_conda ? 'python=3.9 conda-forge::typer=0.3.2 conda-forge::rich=10.6.0 conda-forge::seaborn=0.11.0 conda-forge::pandas=1.3.0 bioconda::bcbio-gff=0.6.6 bioconda::dna_features_viewer=3.0.3' : null)
+ conda 'python=3.9 conda-forge::typer=0.3.2 conda-forge::rich=10.6.0 conda-forge::seaborn=0.11.0 conda-forge::pandas=1.3.0 bioconda::bcbio-gff=0.6.6 bioconda::dna_features_viewer=3.0.3'
  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
  container 'https://depot.galaxyproject.org/singularity/mulled-v2-596f42d854e849eb773ecd1b48f2b698c2d09c9f:400d0a2593841aa0bfa3402fe85debd55a29cf37-0'
  } else {

diff --git a/modules/local/irma.nf b/modules/local/irma.nf
@@ -2,7 +2,7 @@ process IRMA {
  tag "$meta.id"
  label 'process_high'
 
- conda (params.enable_conda ? "bioconda::irma=1.0.2" : null)
+ conda "bioconda::irma=1.0.2"
  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
  container 'https://depot.galaxyproject.org/singularity/irma:1.0.2--pl5321hdfd78af_2'
  } else {

diff --git a/modules/local/medaka.nf b/modules/local/medaka.nf
@@ -5,7 +5,7 @@ process MEDAKA {
  tag "$sample|$segment|$id"
  label 'process_low'
 
- conda (params.enable_conda ? 'bioconda::medaka=1.4.4' : null)
+ conda 'bioconda::medaka=1.4.4'
  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
  container 'https://depot.galaxyproject.org/singularity/medaka:1.4.4--py38h130def0_0'
  } else {

diff --git a/modules/local/minimap2.nf b/modules/local/minimap2.nf
@@ -4,7 +4,7 @@ process MINIMAP2 {
  tag "$sample|$segment|$ref_id"
  label 'process_low'
 
- conda (params.enable_conda ? 'bioconda::minimap2=2.24 bioconda::samtools=1.15' : null)
+ conda 'bioconda::minimap2=2.24 bioconda::samtools=1.15'
  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
  container 'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0'
  } else {

diff --git a/modules/local/misc.nf b/modules/local/misc.nf
@@ -4,7 +4,7 @@ process CAT_NANOPORE_FASTQ {
  tag "${meta.id}"
  label 'process_low'
 
- conda (params.enable_conda ? "conda-forge::pigz=2.6" : null)
+ conda "conda-forge::pigz=2.6"
  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
  container "https://depot.galaxyproject.org/singularity/mulled-v2-2b04072095278721dc9a5772e61e406f399b6030:7c7abf911e92d7fb831611ffb965f3cf7fe2c01d-0"
  } else {
@@ -60,7 +60,7 @@ process CAT_DB {
 
 process CAT_CONSENSUS {
  tag "$sample"
- conda (params.enable_conda ? 'bioconda::shiptv=0.4.0' : null)
+ conda 'bioconda::shiptv=0.4.0'
  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
  container 'https://depot.galaxyproject.org/singularity/shiptv:0.4.0--pyh5e36f6f_0'
  } else {

diff --git a/modules/local/mosdepth.nf b/modules/local/mosdepth.nf
@@ -4,7 +4,7 @@ process MOSDEPTH_GENOME {
  tag "$sample|$segment|$ref_id"
  label 'process_low'
 
- conda (params.enable_conda ? 'bioconda::mosdepth=0.3.3' : null)
+ conda 'bioconda::mosdepth=0.3.3'
  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
  container "https://depot.galaxyproject.org/singularity/mosdepth:0.3.3--h37c5b7d_2"
  } else {

diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf
@@ -1,7 +1,7 @@
 process MULTIQC {
  label 'process_low'
 
- conda (params.enable_conda ? "bioconda::multiqc=1.12" : null)
+ conda "bioconda::multiqc=1.12"
  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
  container 'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0'
  } else {

diff --git a/modules/local/pull_top_ref_id.nf b/modules/local/pull_top_ref_id.nf
@@ -2,7 +2,7 @@ process PULL_TOP_REF_ID {
  tag "$meta.id"
  label 'process_low'
 
- conda (params.enable_conda ? 'conda-forge::python=3.10 conda-forge::biopython=1.80 conda-forge::openpyxl=3.1.0 conda-forge::pandas=1.5.3 conda-forge::rich=12.6.0 conda-forge::typer=0.7.0 conda-forge::xlsxwriter=3.0.8 conda-forge::polars=0.17.9 conda-forge::pyarrow=11.0.0' : null)
+ conda 'conda-forge::python=3.10 conda-forge::biopython=1.80 conda-forge::openpyxl=3.1.0 conda-forge::pandas=1.5.3 conda-forge::rich=12.6.0 conda-forge::typer=0.7.0 conda-forge::xlsxwriter=3.0.8 conda-forge::polars=0.17.9 conda-forge::pyarrow=11.0.0'
  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
  container 'https://depot.galaxyproject.org/singularity/mulled-v2-cfa20dfeb068db79c8620a11753add64c23d013a:019cd79f70be602ca625a1a0a4eabab462611a3a-0'
  } else {

diff --git a/modules/local/seqtk_seq.nf b/modules/local/seqtk_seq.nf
@@ -5,7 +5,7 @@ process SEQTK_SEQ{
  tag "$sample|$segment|$ref_id"
  // use default process resources
 
- conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)
+ conda "bioconda::seqtk=1.3"
  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
  container 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3'
  } else {

diff --git a/modules/local/subtyping_report.nf b/modules/local/subtyping_report.nf
@@ -15,7 +15,7 @@ process SUBTYPING_REPORT {
  "2 GB"
  }
  }
- conda (params.enable_conda ? 'conda-forge::python=3.10 conda-forge::biopython=1.80 conda-forge::openpyxl=3.1.0 conda-forge::pandas=1.5.3 conda-forge::rich=12.6.0 conda-forge::typer=0.7.0 conda-forge::xlsxwriter=3.0.8 conda-forge::polars=0.17.9 conda-forge::pyarrow=11.0.0' : null)
+ conda 'conda-forge::python=3.10 conda-forge::biopython=1.80 conda-forge::openpyxl=3.1.0 conda-forge::pandas=1.5.3 conda-forge::rich=12.6.0 conda-forge::typer=0.7.0 conda-forge::xlsxwriter=3.0.8 conda-forge::polars=0.17.9 conda-forge::pyarrow=11.0.0'
  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
  container 'https://depot.galaxyproject.org/singularity/mulled-v2-cfa20dfeb068db79c8620a11753add64c23d013a:019cd79f70be602ca625a1a0a4eabab462611a3a-0'
  } else {
@@ -39,7 +39,9 @@ process SUBTYPING_REPORT {
  --excel-report nf-flu-subtyping-report.xlsx \\
  --pident-threshold $params.pident_threshold \\
  $blastn_results
+
  ln -s .command.log parse_influenza_blast_results.log
+
  cat <<-END_VERSIONS > versions.yml
  "${task.process}":
  python: \$(python --version | sed 's/Python //g')

diff --git a/modules/local/vcf_filter_frameshift.nf b/modules/local/vcf_filter_frameshift.nf
@@ -2,7 +2,7 @@ process VCF_FILTER_FRAMESHIFT {
  tag "$sample|$segment|$ref_id"
  // use default process resources
 
- conda (params.enable_conda ? 'conda-forge::python=3.9 conda-forge::pandas=1.3.5 conda-forge::typer=0.4.1' : null)
+ conda 'conda-forge::python=3.9 conda-forge::pandas=1.3.5 conda-forge::typer=0.4.1'
  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
  container 'https://depot.galaxyproject.org/singularity/mulled-v2-80c23cbcd32e2891421c54d1899665046feb07ef:77a31e289d22068839533bf21f8c4248ad274b60-0'
  } else {

diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
@@ -2,7 +2,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
  label 'process_low'
 
  // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
- conda (params.enable_conda ? "bioconda::multiqc=1.11" : null)
+ conda "bioconda::multiqc=1.11"
  container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
  'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' :
  'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }"