Merge pull request #77 from nf-core/update-igenomes

Update igenomes config
nf-core · Sep 27, 2023 · 0eacfcf · 0eacfcf
2 parents 984354b + 8a33e67
commit 0eacfcf
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Showing 16 changed files with 531 additions and 405 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.04.0"
+          - "22.10.1"
           - "latest-everything"
 
     steps:
@@ -36,6 +36,35 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      - name: Hash Github Workspace
+        id: hash_workspace
+        run: |
+          echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
+
+      - name: Cache test data
+        id: cache-testdata
+        uses: actions/cache@v3
+        with:
+          path: test-datasets/
+          key: ${{ steps.hash_workspace.outputs.digest }}
+
+      - name: Check out test data
+        if: steps.cache-testdata.outputs.cache-hit != 'true'
+        uses: actions/checkout@v3
+        with:
+          repository: nf-core/test-datasets
+          ref: circrna
+          path: test-datasets/
+
+      - name: Replace remote paths in samplesheets
+        run: |
+          for f in ${{ github.workspace }}/test-datasets/*.csv; do
+            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/circrna/=${{ github.workspace }}/test-datasets/=g" $f
+            echo "========== $f ============"
+            cat $f
+            echo "========================================"
+          done;
+
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets
diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 [![GitHub Actions CI Status](https://github.com/nf-core/circrna/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/circrna/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/nf-core/circrna/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/circrna/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/circrna/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-22aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,8 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/circrna/releases/tag/1.0.0" target="_blank">nf-core/circrna</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/circrna/1.0.0/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/circrna/releases/tag/dev"
+  target="_blank">nf-core/circrna</a> analysis pipeline. For information about how to
+  interpret these results, please see the <a href="https://nf-co.re/circrna/dev/docs/output"
+  target="_blank">documentation</a>.
 
 report_section_order:
   "nf-core-circrna-methods-description":

diff --git a/conf/igenomes.config b/conf/igenomes.config
diff --git a/conf/test.config b/conf/test.config
@@ -15,20 +15,20 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Limit resources so that this can run on GitHub Actions
-    max_cpus = 2
-    max_memory = 6.GB
-    max_time = 6.h
+    max_cpus                   = 2
+    max_memory                 = 6.GB
+    max_time                   = 6.h
 
     // Input data for test data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/circrna/samples.csv'
-    fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/circrna/reference/chrI.fa'
-    gtf = 'https://raw.githubusercontent.com/nf-core/test-datasets/circrna/reference/chrI.gtf'
-    mature = 'https://raw.githubusercontent.com/nf-core/test-datasets/circrna/reference/mature.fa'
-    tool = 'circexplorer2'
-    phenotype = 'https://raw.githubusercontent.com/nf-core/test-datasets/circrna/phenotype.csv'
-    skip_trimming = false
-    module = 'circrna_discovery,mirna_prediction,differential_expression'
-    outdir = 'results/'
-    bsj_reads = 2
-    species = 'cel'
+    input                      = 'https://raw.githubusercontent.com/nf-core/test-datasets/circrna/samples.csv'
+    fasta                      = 'https://raw.githubusercontent.com/nf-core/test-datasets/circrna/reference/chrI.fa'
+    gtf                        = 'https://raw.githubusercontent.com/nf-core/test-datasets/circrna/reference/chrI.gtf'
+    mature                     = 'https://raw.githubusercontent.com/nf-core/test-datasets/circrna/reference/mature.fa'
+    tool                       = 'circexplorer2'
+    phenotype                  = 'https://raw.githubusercontent.com/nf-core/test-datasets/circrna/phenotype.csv'
+    skip_trimming              = false
+    module                     = 'circrna_discovery,mirna_prediction,differential_expression'
+    outdir                     = 'results/'
+    bsj_reads                  = 2
+    species                    = 'cel'
 }
diff --git a/conf/test_cache.config b/conf/test_cache.config
@@ -0,0 +1,34 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/circrna -profile test,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus                   = 2
+    max_memory                 = 6.GB
+    max_time                   = 6.h
+
+    // Test input data
+    input                      = "${params.test_data_base}/samples.csv"
+    fasta                      = "${params.test_data_base}/reference/chrI.fa"
+    gtf                        = "${params.test_data_base}/reference/chrI.gtf"
+    mature                     = "${params.test_data_base}/reference/mature.fa"
+    tool                       = "circexplorer2"
+    phenotype                  = "${params.test_data_base}/phenotype.csv"
+    skip_trimming              = false
+    module                     = "circrna_discovery,mirna_prediction,differential_expression"
+    outdir                     = "results/"
+    bsj_reads                  = 2
+    species                    = "cel"
+}
diff --git a/main.nf b/main.nf
@@ -17,10 +17,14 @@ nextflow.enable.dsl = 2
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-// TODO nf-core: Remove this line if you don't need a FASTA file
-//   This is an example of how to use getGenomeAttribute() to fetch parameters
-//   from igenomes.config using `--genome`
-params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
+params.fasta   = WorkflowMain.getGenomeAttribute(params, 'fasta')
+params.gtf     = WorkflowMain.getGenomeAttribute(params, 'gtf')
+params.bwa     = WorkflowMain.getGenomeAttribute(params, 'bwa')
+params.star    = WorkflowMain.getGenomeAttribute(params, 'star')
+params.bowtie  = WorkflowMain.getGenomeAttribute(params, 'bowtie')
+params.bowtie2 = WorkflowMain.getGenomeAttribute(params, 'bowtie2')
+params.mature  = WorkflowMain.getGenomeAttribute(params, 'mature')
+params.species = WorkflowMain.getGenomeAttribute(params, 'species_id')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/modules/local/circexplorer2/filter/main.nf b/modules/local/circexplorer2/filter/main.nf
@@ -5,7 +5,7 @@ process CIRCEXPLORER2_FILTER {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(txt)

diff --git a/modules/local/ciriquant/filter/main.nf b/modules/local/ciriquant/filter/main.nf
@@ -5,7 +5,7 @@ process CIRIQUANT_FILTER {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(gtf)

diff --git a/modules/local/dcc/filter/main.nf b/modules/local/dcc/filter/main.nf
@@ -5,7 +5,7 @@ process DCC_FILTER {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(txt)

diff --git a/modules/local/segemehl/filter/main.nf b/modules/local/segemehl/filter/main.nf
@@ -5,7 +5,7 @@ process SEGEMEHL_FILTER {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(results)

diff --git a/modules/local/star/sjdb/main.nf b/modules/local/star/sjdb/main.nf
@@ -4,7 +4,7 @@ process SJDB {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     path(sjdb)

diff --git a/modules/local/stringtie/prepde/main.nf b/modules/local/stringtie/prepde/main.nf
@@ -19,7 +19,7 @@ process STRINGTIE_PREPDE {
 
     script:
     """
-    for file in \$(ls *.gtf); do sample_id=\${file%".transcripts.gtf"}; touch samples.txt; printf "\$sample_id\t\$file\n" >> samples.txt ; done
+    for file in \$(ls *.gtf); do sample_id=\${file%".transcripts.gtf"}; touch samples.txt; printf "\$sample_id\t\$file\\n" >> samples.txt ; done
 
     prepDE.py -i samples.txt
 

diff --git a/modules/local/targetscan/database/main.nf b/modules/local/targetscan/database/main.nf
@@ -5,7 +5,7 @@ process TARGETSCAN_DATABASE {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     path(mature)

diff --git a/nextflow.config b/nextflow.config
@@ -27,16 +27,9 @@ params {
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes'
     igenomes_ignore            = false
-    bowtie                     = null
-    bowtie2                    = null
-    bwa                        = null
     hisat2                     = null
     hisat2_build_memory        = '200.GB'
     segemehl                   = null
-    star                       = null
-    gtf                        = null
-    mature                     = null
-    species                    = null
     save_reference             = true
 
     // Trimming
@@ -219,8 +212,9 @@ profiles {
         executor.cpus          = 4
         executor.memory        = 8.GB
     }
-    test      { includeConfig 'conf/test.config'      }
-    test_full { includeConfig 'conf/test_full.config' }
+    test       { includeConfig 'conf/test.config'      }
+    test_full  { includeConfig 'conf/test_full.config' }
+    test_cache { includeConfig 'conf/test_cache.config' }
 }
 
 // Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
@@ -280,8 +274,8 @@ manifest {
     homePage        = 'https://github.com/nf-core/circrna'
     description     = """Quantification, miRNA target prediction and differential expression analysis of circular RNAs"""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=23.04.0'
-    version         = '1.0.0'
+    nextflowVersion = '!>=22.10.1'
+    version         = 'dev'
     doi             = ''
 }
 

diff --git a/workflows/circrna.nf b/workflows/circrna.nf
@@ -50,16 +50,6 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
 // Check mandatory parameters
 if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
 
-// Genome params
-params.fasta   = params.genome  ? params.genomes[ params.genome ].fasta ?: false : false
-params.gtf     = params.genome  ? params.genomes[ params.genome ].gtf ?: false : false
-params.bwa     = params.genome && params.tool.contains('ciriquant') ? params.genomes[ params.genome ].bwa ?: false : false
-params.star    = params.genome && ( params.tool.contains('circexplorer2') || params.tool.contains('dcc') || params.tool.contains('circrna_finder') ) ? params.genomes[ params.genome ].star ?: false : false
-params.bowtie  = params.genome && params.tool.contains('mapsplice') ? params.genomes[ params.genome ].bowtie ?: false : false
-params.bowtie2 = params.genome && params.tool.contains('find_circ') ? params.genomes[ params.genome ].bowtie2 ?: false : false
-params.mature  = params.genome && params.module.contains('mirna_prediction') ? params.genomes[ params.genome ].mature ?: false : false
-params.species = params.genome  ? params.genomes[ params.genome ].species_id ?: false : false
-
 ch_phenotype   = params.phenotype && params.module.contains('differential_expression') ? file(params.phenotype, checkIfExists:true) : Channel.empty()
 ch_fasta       = params.fasta ? file(params.fasta) : 'null'
 ch_gtf         = params.gtf ? file(params.gtf) : 'null'