run pipeline tests with singularity and conda too

.github/workflows/ci.yml

@@ -48,6 +48,7 @@ jobs:
             profile: "conda"
           - isMaster: false
             profile: "singularity"
+      fail-fast: false # run all tests even if one fails
 
     steps:
       - name: Check out pipeline code
@@ -88,4 +89,4 @@ jobs:
 
       - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results_${{ matrix.test_name }}
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results_${{ matrix.test_name }}_${{ matrix.profile }}

CHANGELOG.md

@@ -19,6 +19,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Make output of FluteMLE optional as when some pathways produce bugs some channels are then empty ([#190](https://github.com/nf-core/crisprseq/pull/190))
 - Fix a typo in crisprcleanr/normalize, when a user inputs a file ([#192](https://github.com/nf-core/crisprseq/pull/192))
 
+### General
+
+- Run pipeline tests with docker, singularity and conda on CI ([#185](https://github.com/nf-core/crisprseq/pull/185))
+
 ## [v2.2.1 Romarin Curie - patch](https://github.com/nf-core/crisprseq/releases/tag/2.2.1) - [23.07.2024]
 
 ### Fixed

README.md

@@ -104,6 +104,10 @@ nextflow run nf-core/crisprseq --input samplesheet.csv --analysis <targeted/scre
 > [!WARNING]
 > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).
 
+> [!WARNING]
+> Since Nextflow 23.07.0, Nextflow no longer mounts the host's HOME directory when using Apptainer or Singularity. MAGeCKFlute needs HOME directory write access. As a workaround, you can revert to the old behavior by setting the environment variable NXF_APPTAINER_HOME_MOUNT or NXF_SINGULARITY_HOME_MOUNT to true in the machine from which you launch the pipeline.
+> `export NXF_SINGULARITY_HOME_MOUNT=true; nextflow run nf-core/crisprseq --input samplesheet.csv --analysis screening --outdir <OUTDIR> -profile <singularity/aptainer>`
+
 For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/crisprseq/usage) and the [parameter documentation](https://nf-co.re/crisprseq/parameters).
 
 ## Pipeline output

conf/modules.config

@@ -317,7 +317,7 @@ process {
     }
 
     withName: MEDAKA {
-        ext.args = '-m r941_min_high_g303'
+        ext.args = { "-m ${model}" }
         ext.prefix = { "${reads.baseName}_medakaConsensus" }
     }
 

modules.json

@@ -95,7 +95,8 @@
                     "racon": {
                         "branch": "master",
                         "git_sha": "f5ed3ac0834b68e80a00a06a61d04ce8e896f275",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/racon/racon.diff"
                     },
                     "samtools/index": {
                         "branch": "master",

modules/local/mageck/flutemle.nf

@@ -3,10 +3,10 @@ process MAGECK_FLUTEMLE {
     tag "$prefix"
     label 'process_high'
 
-    conda "bioconda::bioconductor-mageckflute=2.2.0"
+    conda "bioconda::bioconductor-mageckflute==2.6.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-mageckflute:2.2.0--r42hdfd78af_0':
-        'biocontainers/bioconductor-mageckflute:2.2.0--r42hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-mageckflute:2.6.0--r43hdfd78af_0':
+        'biocontainers/bioconductor-mageckflute:2.6.0--r43hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gene_summary)

modules/local/mageck/graphrra.nf

@@ -2,10 +2,10 @@ process MAGECK_GRAPHRRA {
     tag "$meta.treatment"
     label 'process_single'
 
-    conda "bioconda::bioconductor-mageckflute=2.2.0"
+    conda "bioconda::bioconductor-mageckflute==2.6.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mageckflute:2.2.0--r42hdfd78af_0':
-        'biocontainers/bioconductor-mageckflute:2.2.0--r42hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-mageckflute:2.6.0--r43hdfd78af_0':
+        'biocontainers/bioconductor-mageckflute:2.6.0--r43hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gene_summary)

modules/local/matricescreation.nf

@@ -1,7 +1,7 @@
 process MATRICESCREATION {
     label 'process_single'
 
-    conda 'r-ggplot2=3.4.3 bioconductor-shortread=1.58.0 r-ggpubr=0.6.0 r-ggmsa=1.0.2 r-seqmagick=0.1.6 r-tidyr=1.3.0 r-ggseqlogo=0.1 r-cowplot=1.1.1 r-seqinr=4.2_30 r-optparse=1.7.3 r-dplyr=1.1.2 r-plyr=1.8.8 r-stringr=1.5.0 r-plotly=4.10.2'
+    conda 'conda-forge::r-base==4.0'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-6de07928379e6eface08a0019c4a1d6b5192e805:0d77388f37ddd923a087f7792e30e83ab54c918c-0' :
         'biocontainers/mulled-v2-6de07928379e6eface08a0019c4a1d6b5192e805:0d77388f37ddd923a087f7792e30e83ab54c918c-0' }"

modules/local/orient_reference.nf

@@ -2,7 +2,8 @@ process ORIENT_REFERENCE {
     tag "$meta.id"
     label 'process_single'
 
-    conda "r-seqinr=4.2_16 bioconductor-biostrings=2.62.0 bioconductor-shortread=1.52.0"
+    // jpeg is required in the conda container to fix a "libjpeg.so.9: No such file or directory" error
+    conda "r-seqinr=4.2_16 bioconductor-biostrings=2.62.0 bioconductor-shortread=1.52.0 jpeg=9d"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-63136bce0d642de81864be727b6b42a26026e33b:d3ce5caf7bcbf6cecedcf51b0135646831c01e77-0' :
         'biocontainers/mulled-v2-63136bce0d642de81864be727b6b42a26026e33b:d3ce5caf7bcbf6cecedcf51b0135646831c01e77-0' }"

modules/local/venndiagram.nf

@@ -3,7 +3,7 @@ process VENNDIAGRAM {
     label 'process_low'
 
 
-    conda "bioconda::r-venndiagram=1.6.16"
+    conda "conda-forge::r-ggvenn=0.1.10"
     container "ghcr.io/qbic-pipelines/rnadeseq:dev"
 
     input:

nextflow.config

@@ -43,7 +43,7 @@ params {
 
     // UMI parameters
     umi_bin_size               = 1
-    medaka_model               = 'r941_min_high_g303'
+    medaka_model               = 'https://github.com/nanoporetech/medaka/raw/master/medaka/data/r941_min_high_g303_model.hdf5'
 
     // Vsearch options
     vsearch_minseqlength       = 55

nextflow_schema.json

@@ -88,7 +88,7 @@
                 },
                 "medaka_model": {
                     "type": "string",
-                    "default": "r941_min_high_g303",
+                    "default": "https://github.com/nanoporetech/medaka/raw/master/medaka/data/r941_min_high_g303_model.hdf5",
                     "fa_icon": "fas fa-font",
                     "description": "Medaka model (-m) to use according to the basecaller used."
                 }

templates/template_fluteMLE.R

@@ -4,6 +4,14 @@
     ####
     #### graphs mageck MLE
 
+    # Required to fix corrupted cache from Singularity container
+    library(BiocFileCache)
+    bfc <- BiocFileCache("~/.cache/R/ExperimentHub")
+    res <- bfcquery(bfc, "experimenthub.index.rds", field="rname", exact=TRUE)
+    bfcremove(bfc, rids=res\$rid)
+    library(ExperimentHub)
+    eh = ExperimentHub()
+
     library(MAGeCKFlute)
     library(clusterProfiler)
     library(ggplot2)

workflows/crisprseq_targeted.nf

@@ -507,7 +507,8 @@ workflow CRISPRSEQ_TARGETED {
         //
         MEDAKA (
             ch_clusters_sequence
-                .join(RACON_2.out.improved_assembly)
+                .join(RACON_2.out.improved_assembly),
+            Channel.value( file(params.medaka_model) )
         )
         ch_versions = ch_versions.mix(MEDAKA.out.versions.first())