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fix testdata file #120

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merged 4 commits into from
Nov 30, 2021
Merged

fix testdata file #120

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3de3726
add new container for edger
lpantano Nov 11, 2021
0f4da15
Merge branch 'dev' of github.com:nf-core/smrnaseq into dev
lpantano Nov 12, 2021
5a65851
fix path to test data
lpantano Nov 23, 2021
59ffb03
update changelog and bump to 2.0.0dev
lpantano Nov 23, 2021
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4 changes: 3 additions & 1 deletion CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,7 +1,9 @@
# nf-core/smrnaseq: Changelog

## v1.3.0dev - [2021-09-15]
## v2.0.0dev - [2021-09-15]
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😍

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Yes I think a 2.0.0 is justified here!


* 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
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19 changes: 5 additions & 14 deletions conf/test.config
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Expand Up @@ -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'
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Maybe we could implement a similar versioning such as in the rnaseq pipeline e.g. https://github.com/nf-core/test-datasets/tree/rnaseq/samplesheet/v3.4

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Great idea, especially if some potential future changes are coming in that might have to adjust the format at some point again 👍🏻

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ok, should I merge and then coordinate this? or do you want to do it now?

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

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2 changes: 1 addition & 1 deletion conf/test_full.config
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Expand Up @@ -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"
}
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6 changes: 3 additions & 3 deletions modules/local/mirtop_quant.nf
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Expand Up @@ -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:
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