PROFILES: test -> test_cache + restore test

.github/workflows/ci.yml

@@ -66,7 +66,7 @@ jobs:
 
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
+          nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
 
   star_salmon:
     name: Test STAR Salmon with workflow parameters
@@ -128,7 +128,7 @@ jobs:
 
       - name: Run pipeline with STAR and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
+          nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
 
   star_rsem:
     name: Test STAR RSEM with workflow parameters
@@ -179,7 +179,7 @@ jobs:
 
       - name: Run pipeline with RSEM STAR and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
+          nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
 
   hisat2:
     name: Test HISAT2 with workflow parameters
@@ -230,7 +230,7 @@ jobs:
 
       - name: Run pipeline with HISAT2 and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
+          nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
 
   salmon:
     name: Test Salmon with workflow parameters
@@ -281,4 +281,4 @@ jobs:
 
       - name: Run pipeline with Salmon and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
+          nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/

conf/test.config

@@ -21,20 +21,19 @@ params {
 
 
     // Input data
-    // params.test_data_base (default) = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/'
-    input = "${params.test_data_base}/samplesheet/v3.10/samplesheet_test.csv"
+    input = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/v3.10/samplesheet_test.csv"
 
     // Genome references
-    fasta              = "${params.test_data_base}/reference/genome.fasta"
-    gtf                = "${params.test_data_base}/reference/genes.gtf.gz"
-    gff                = "${params.test_data_base}/reference/genes.gff.gz"
-    transcript_fasta   = "${params.test_data_base}/reference/transcriptome.fasta"
-    additional_fasta   = "${params.test_data_base}/reference/gfp.fa.gz"
-
-    bbsplit_fasta_list = "${params.test_data_base}/reference/bbsplit_fasta_list.txt"
-    hisat2_index       = "${params.test_data_base}/reference/hisat2.tar.gz"
-    salmon_index       = "${params.test_data_base}/reference/salmon.tar.gz"
-    rsem_index         = "${params.test_data_base}/reference/rsem.tar.gz"
+    fasta              = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genome.fasta"
+    gtf                = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genes.gtf.gz"
+    gff                = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genes.gff.gz"
+    transcript_fasta   = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/transcriptome.fasta"
+    additional_fasta   = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/gfp.fa.gz"
+
+    bbsplit_fasta_list = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/bbsplit_fasta_list.txt"
+    hisat2_index       = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/hisat2.tar.gz"
+    salmon_index       = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/salmon.tar.gz"
+    rsem_index         = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/rsem.tar.gz"
 
     // Other parameters
     skip_bbsplit        = false

conf/test_cache.config

@@ -0,0 +1,50 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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/rnaseq -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'
+
+
+    // Input data
+    // params.test_data_base (default) = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/'
+    input = "${params.test_data_base}/samplesheet/v3.10/samplesheet_test.csv"
+
+    // Genome references
+    fasta              = "${params.test_data_base}/reference/genome.fasta"
+    gtf                = "${params.test_data_base}/reference/genes.gtf.gz"
+    gff                = "${params.test_data_base}/reference/genes.gff.gz"
+    transcript_fasta   = "${params.test_data_base}/reference/transcriptome.fasta"
+    additional_fasta   = "${params.test_data_base}/reference/gfp.fa.gz"
+
+    bbsplit_fasta_list = "${params.test_data_base}/reference/bbsplit_fasta_list.txt"
+    hisat2_index       = "${params.test_data_base}/reference/hisat2.tar.gz"
+    salmon_index       = "${params.test_data_base}/reference/salmon.tar.gz"
+    rsem_index         = "${params.test_data_base}/reference/rsem.tar.gz"
+
+    // Other parameters
+    skip_bbsplit        = false
+    pseudo_aligner      = 'salmon'
+    umitools_bc_pattern = 'NNNN'
+}
+
+// When using RSEM, remove warning from STAR whilst building tiny indices
+process {
+    withName: 'RSEM_PREPAREREFERENCE_GENOME' {
+        ext.args2 = "--genomeSAindexNbases 7"
+    }
+}

nextflow.config

@@ -233,8 +233,9 @@ profiles {
     public_aws_ecr {
         includeConfig 'conf/public_aws_ecr.config'
     }
-    test          { includeConfig 'conf/test.config'      }
-    test_full     { includeConfig 'conf/test_full.config' }
+    test          { includeConfig 'conf/test.config'       }
+    test_cache    { includeConfig 'conf/test_cache.config' }
+    test_full     { includeConfig 'conf/test_full.config'  }
     test_full_aws { 
         includeConfig 'conf/test_full.config' 
     }