diff --git a/CHANGELOG.md b/CHANGELOG.md index 38e3abdf..04a126b6 100644 --- 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 index 77979625..0bfa6567 100644 --- 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 index 7d042c6a..ec1ef3f2 100644 --- 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 index 8a7ed754..7bdb5946 100644 --- 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: