Merge pull request #120 from nf-core/lpantano-patch-fix-testdata-file

fix testdata file
nf-core · Nov 30, 2021 · e979ed2 · e979ed2
2 parents 3e25b1c + 59ffb03
commit e979ed2
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Showing 4 changed files with 12 additions and 19 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,7 +1,9 @@
 # nf-core/smrnaseq: Changelog
 
-## v1.3.0dev - [2021-09-15]
+## v2.0.0dev - [2021-09-15]
 
+* Point to the proper test data branch
+* Update mirtop container
 * Software version(s) will now be reported for every module imported during a given pipeline execution
 * Adapted DSL 2.0
 * Updated `nextflow_schema.json` should now display correctly on Nextflow Tower

diff --git a/conf/test.config b/conf/test.config
@@ -20,21 +20,12 @@ params {
     max_time   = 6.h
 
     // Input data
-    //   input = 'https://raw.githubusercontent.com/nf-core/test-datasets/smrnaseq/testdata/samplesheet.csv'
-    // Genome references
- //   bt_indices = [
- //     'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference'
- //   ]
- //   gtf = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/genes.gtf'
- //   mature = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/mature.fa'
- //   hairpin = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/hairpin.fa'
- //   mirna_gtf = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/hsa.gff3'
 
-    input = 'https://github.com/nf-core/test-datasets/raw/smrnaseq-better-input/testdata/samplesheet.csv'
-    fasta = 'https://github.com/nf-core/test-datasets/raw/smrnaseq-better-input/reference/genome.fa'
-    mature = 'https://github.com/nf-core/test-datasets/raw/smrnaseq-better-input/reference/mature.fa'
-    hairpin = 'https://github.com/nf-core/test-datasets/raw/smrnaseq-better-input/reference/hairpin.fa'
-    mirna_gtf = 'https://github.com/nf-core/test-datasets/raw/smrnaseq-better-input/reference/hsa.gff3'
+    input = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/testdata/samplesheet.csv'
+    fasta = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/genome.fa'
+    mature = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/mature.fa'
+    hairpin = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/hairpin.fa'
+    mirna_gtf = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/hsa.gff3'
     mirtrace_species = "hsa"
     skip_mirdeep = true
 

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -17,7 +17,7 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    input = 'https://github.com/nf-core/test-datasets/raw/smrnaseq-better-input/testdata/samplesheet.csv'
+    input = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/testdata/samplesheet.csv'
     genome = 'GRCh37'
     mirtrace_species = "hsa"
 }

diff --git a/modules/local/mirtop_quant.nf b/modules/local/mirtop_quant.nf
@@ -10,11 +10,11 @@ process MIRTOP_QUANT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:".", meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? 'bioconda::mirtop=0.4.23 bioconda::samtools=1.13 conda-base::r-base=4.0.3' : null)
+    conda (params.enable_conda ? 'bioconda::mirtop=0.4.24 bioconda::samtools=1.13 conda-base::r-base=4.0.3' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/mulled-v2-1f73c7bc18ac86871db9ef0a657fb39d6cbe1cf5:dd7c9649e165d535c1dd2c162ec900e7206398ec-0"
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:c8b426b3677a47f58bbbc443c0cf67bf8d53a97b-0"
     } else {
-        container "quay.io/biocontainers/mulled-v2-1f73c7bc18ac86871db9ef0a657fb39d6cbe1cf5:dd7c9649e165d535c1dd2c162ec900e7206398ec-0"
+        container "quay.io/biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:c8b426b3677a47f58bbbc443c0cf67bf8d53a97b-0"
     }
 
     input: