Merge branch 'master' into workflow-output-dsl

Signed-off-by: Ben Sherman <[email protected]>

.github/workflows/build.yml

@@ -35,3 +35,10 @@ jobs:
           ./nextflow run . -profile docker
         env:
           NXF_ANSI_LOG: false
+
+      - name: Tests Wave
+        run: |
+          curl -fsSL get.nextflow.io | bash
+          ./nextflow run . -profile docker,wave
+        env:
+          NXF_ANSI_LOG: false

README.md

@@ -15,7 +15,7 @@ implemented with Nextflow.
 
 1. If you don't have it already install Docker in your computer. Read more [here](https://docs.docker.com/).
 
-2. Install Nextflow (version 23.04.0 or later):
+2. Install Nextflow (version 23.10.0 or later):
 
         curl -s https://get.nextflow.io | bash
 

conda.yml

@@ -1,10 +1,8 @@
 name: rnaseq-nf
 channels:
-  - seqera
-  - bioconda
-  - conda-forge
-  - defaults
+- conda-forge
+- bioconda
 dependencies:
-  - salmon=1.10.2
-  - fastqc=0.12.1
-  - multiqc=1.15
+- bioconda::fastqc=0.12.1
+- bioconda::multiqc=1.25
+- bioconda::salmon=1.10.3

docker/Dockerfile

@@ -1,16 +1,14 @@
-FROM mambaorg/micromamba
+#
+# don't waste your time with this
+# use seqera containers https://seqera.io/containers/
+#
+FROM mambaorg/micromamba:1.5.10-noble
 MAINTAINER Paolo Di Tommaso <[email protected]>
 
-RUN \
-   micromamba install -y -n base -c defaults -c bioconda -c conda-forge \
-      salmon=1.10.2 \
-      fastqc=0.12.1 \
-      multiqc=1.17 \
-      python=3.11 \
-      typing_extensions \
-      importlib_metadata \
-      procps-ng \
-   && micromamba clean -a -y
+COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
+RUN micromamba install -y -n base -f /tmp/conda.yml \
+    && micromamba install -y -n base conda-forge::procps-ng \
+    && micromamba clean -a -y
 
 ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
 USER root

docker/Makefile

@@ -1,10 +1,10 @@
-version ?= v1.2.1
+version ?= v1.3.0
 
 all: build push
 
 build:
 	cp ../conda.yml .
-	docker build --output=type=docker --progress=plain --tag quay.io/nextflow/rnaseq-nf:${version} .
+	docker build --output=type=docker --progress=plain --tag docker.io/nextflow/rnaseq-nf:${version} .
 
 push:
-	docker push quay.io/nextflow/rnaseq-nf:${version}
+	docker push docker.io/nextflow/rnaseq-nf:${version}

main.nf

@@ -1,29 +1,9 @@
 #!/usr/bin/env nextflow 
 
-/* 
- * Copyright (c) 2013-2023, Seqera Labs.
- *
- * This Source Code Form is subject to the terms of the Mozilla Public
- * License, v. 2.0. If a copy of the MPL was not distributed with this
- * file, You can obtain one at http://mozilla.org/MPL/2.0/. 
- * 
- * This Source Code Form is "Incompatible With Secondary Licenses", as
- * defined by the Mozilla Public License, v. 2.0.
- */
-
 /*
  * Proof of concept of a RNAseq pipeline implemented with Nextflow
- *
- * Authors:
- * - Paolo Di Tommaso <[email protected]>
- * - Emilio Palumbo <[email protected]>
- * - Evan Floden <[email protected]>
  */
 
-/* 
- * enables modules 
- */
-nextflow.enable.dsl = 2
 
 nextflow.preview.output = true
 
@@ -37,13 +17,6 @@ params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bp
 params.outdir = "results"
 params.multiqc = "$baseDir/multiqc"
 
-log.info """\
- R N A S E Q - N F   P I P E L I N E
- ===================================
- transcriptome: ${params.transcriptome}
- reads        : ${params.reads}
- outdir       : ${params.outdir}
- """
 
 // import modules
 include { RNASEQ } from './modules/rnaseq'
@@ -53,6 +26,15 @@ include { MULTIQC } from './modules/multiqc'
  * main script flow
  */
 workflow {
+
+log.info """\
+  R N A S E Q - N F   P I P E L I N E
+  ===================================
+  transcriptome: ${params.transcriptome}
+  reads        : ${params.reads}
+  outdir       : ${params.outdir}
+  """
+
   read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true ) 
   RNASEQ( params.transcriptome, read_pairs_ch )
   MULTIQC( RNASEQ.out, params.multiqc )

modules/fastqc/main.nf

@@ -1,17 +1,14 @@
 
 process FASTQC {
     tag "FASTQC on $sample_id"
-    conda 'fastqc=0.12.1'
+    conda 'bioconda::fastqc=0.12.1'
 
     input:
     tuple val(sample_id), path(reads)
 
     output:
     path "fastqc_${sample_id}_logs", emit: logs
 
-    publish:
-    logs >> 'fastqc'
-
     script:
     """
     fastqc.sh "$sample_id" "$reads"

modules/index/main.nf

@@ -1,7 +1,7 @@
 
 process INDEX {
     tag "$transcriptome.simpleName"
-    conda 'salmon=1.10.2'
+    conda 'bioconda::salmon=1.10.3'
 
     input:
     path transcriptome 

modules/multiqc/main.nf

@@ -1,13 +1,13 @@
 
 process MULTIQC {
-    conda 'multiqc=1.17'
+    conda 'bioconda::multiqc=1.25'
 
     input:
-    path('*') 
-    path(config) 
+    path '*'
+    path config
 
     output:
-    path('multiqc_report.html'), emit: report
+    path 'multiqc_report.html', emit: report
 
     publish:
     report >> 'multiqc'
@@ -16,6 +16,6 @@ process MULTIQC {
     """
     cp $config/* .
     echo "custom_logo: \$PWD/logo.png" >> multiqc_config.yaml
-    multiqc .
+    multiqc -o multiqc_report.html .
     """
 }

modules/quant/main.nf

@@ -1,7 +1,7 @@
 
 process QUANT {
     tag "$pair_id"
-    conda 'salmon=1.10.2'
+    conda 'bioconda::salmon=1.10.3'
 
     input:
     path index 

nextflow.config

@@ -9,68 +9,82 @@
  * defined by the Mozilla Public License, v. 2.0.
  *
  */
- 
+
 manifest {
-  description = 'Proof of concept of a RNA-seq pipeline implemented with Nextflow' 
+  description = 'Proof of concept of a RNA-seq pipeline implemented with Nextflow'
   author = 'Paolo Di Tommaso'
   nextflowVersion = '>=23.10.0'
 }
 
-/* 
- * default params 
+/*
+ * default params
  */
- 
+
 params.outdir = "results"
 params.reads = "${projectDir}/data/ggal/ggal_gut_{1,2}.fq"
 params.transcriptome = "${projectDir}/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
 params.multiqc = "${projectDir}/multiqc"
 
-/* 
- * defines execution profiles for different environments  
- */ 
+/*
+ * defines execution profiles for different environments
+ */
 
 profiles {
   standard {
-    process.container = 'quay.io/nextflow/rnaseq-nf:v1.2.1'
+    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
   }
 
-  /*
-   * NOTE: requires nextflow 24.03.0-edge or later
-   */
-  wave {
+  'all-reads' {
+    params.reads = "${projectDir}/data/ggal/ggal_*_{1,2}.fq"
+  }
+
+  'wave' {
+    // note: requires nextflow 24.03.0-edge or later
     wave.enabled = true
     wave.strategy = 'conda'
     wave.freeze = true
-    apptainer.ociAutoPull = true
-    singularity.ociAutoPull = true
   }
 
-  docker {
-    process.container = 'quay.io/nextflow/rnaseq-nf:v1.2.1'
+  'wave-mirror' {
+    // note: requires nextflow 24.09.0-edge or later
+    wave.enabled = true
+    wave.strategy = 'container'
+    wave.mirror = true
+    wave.build.repository = 'quay.io'
+  }
+
+  'docker' {
+    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
     docker.enabled = true
   }
 
-  singularity {
-    process.container = 'quay.io/nextflow/rnaseq-nf:v1.2.1'
+  'singularity' {
+    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
     singularity.enabled = true
     singularity.autoMounts = true
   }
 
-  conda {
+  'conda' {
     conda.enabled = true
-    conda.channels = 'seqera,conda-forge,bioconda,defaults'
+    conda.channels = 'conda-forge,bioconda'
   }
-
-  slurm {
-    process.container = 'quay.io/nextflow/rnaseq-nf:v1.2.1'
+
+  'mamba' {
+    conda.enabled = true
+    conda.useMicromamba = true
+    conda.channels = 'conda-forge,bioconda'
+  }
+
+  'slurm' {
+    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
     process.executor = 'slurm'
     singularity.enabled = true
   }
-  
-  batch {
+
+  'batch' {
     params.reads = 's3://rnaseq-nf/data/ggal/lung_{1,2}.fq'
     params.transcriptome = 's3://rnaseq-nf/data/ggal/transcript.fa'
-    process.container = 'quay.io/nextflow/rnaseq-nf:v1.2.1'
+    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
     process.executor = 'awsbatch'
     process.queue = 'nextflow-ci'
     workDir = 's3://nextflow-ci/work'
@@ -79,47 +93,37 @@ profiles {
   }
 
   's3-data' {
-    process.container = 'quay.io/nextflow/rnaseq-nf:v1.2.1'
+    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
     params.reads = 's3://rnaseq-nf/data/ggal/lung_{1,2}.fq'
     params.transcriptome = 's3://rnaseq-nf/data/ggal/transcript.fa'
-  } 
+  }
 
-  gls {
-      params.transcriptome = 'gs://rnaseq-nf/data/ggal/transcript.fa'
-      params.reads = 'gs://rnaseq-nf/data/ggal/gut_{1,2}.fq'
-      params.multiqc = 'gs://rnaseq-nf/multiqc'
-      process.executor = 'google-lifesciences'
-      process.container = 'quay.io/nextflow/rnaseq-nf:v1.2.1'
-      workDir = 'gs://rnaseq-nf/scratch' // <- replace with your own bucket!
-      google.region  = 'europe-west2'
-  } 
-
-  gcb {
+  'google-batch' {
       params.transcriptome = 'gs://rnaseq-nf/data/ggal/transcript.fa'
       params.reads = 'gs://rnaseq-nf/data/ggal/gut_{1,2}.fq'
       params.multiqc = 'gs://rnaseq-nf/multiqc'
       process.executor = 'google-batch'
-      process.container = 'quay.io/nextflow/rnaseq-nf:v1.2.1'
+      process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
       workDir = 'gs://rnaseq-nf/scratch' // <- replace with your own bucket!
       google.region  = 'europe-west2'
   }
 
   'gs-data' {
-      process.container = 'quay.io/nextflow/rnaseq-nf:v1.2.1'
+      process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
       params.transcriptome = 'gs://rnaseq-nf/data/ggal/transcript.fa'
       params.reads = 'gs://rnaseq-nf/data/ggal/gut_{1,2}.fq'
   }
 
-  azb {
-    process.container = 'quay.io/nextflow/rnaseq-nf:v1.2.1'
+  'azure-batch' {
+    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
     workDir = 'az://nf-scratch/work'
     process.executor = 'azurebatch'
     process.queue = 'nextflow-ci' // replace with your own Azure pool name
 
     azure {
       batch {
         location = 'westeurope'
-        accountName = "$AZURE_BATCH_ACCOUNT_NAME" 
+        accountName = "$AZURE_BATCH_ACCOUNT_NAME"
         accountKey = "$AZURE_BATCH_ACCOUNT_KEY"
         autoPoolMode = true
         deletePoolsOnCompletion = true