From 635ab21bc4751826eb46c601597a9af4b59906df Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 15 Nov 2023 18:34:41 +0000 Subject: [PATCH 1/7] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5b5e0e7ef..b5bfd28e6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,8 @@ Special thanks to the following for their contributions to the release: - [Júlia Mir Pedrol](https://github.com/mirpedrol) - [Matthias Zepper](https://github.com/MatthiasZepper) - [Maxime Garcia](https://github.com/maxulysse) +- [Steffen Möller](https://github.com/maxulysse) +- [hmehlan](https://github.com/hmehlan) Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. From cc3bc72be3d6deafaaa5925dca10bd540a3685d6 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 15 Nov 2023 22:30:24 +0000 Subject: [PATCH 2/7] fix credits --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b5bfd28e6..ddeda910f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,12 +10,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 Special thanks to the following for their contributions to the release: - [Adam Talbot](https://github.com/adamrtalbot) +- [hmehlan](https://github.com/hmehlan) - [Jonathan Manning](https://github.com/pinin4fjords) - [Júlia Mir Pedrol](https://github.com/mirpedrol) - [Matthias Zepper](https://github.com/MatthiasZepper) - [Maxime Garcia](https://github.com/maxulysse) -- [Steffen Möller](https://github.com/maxulysse) -- [hmehlan](https://github.com/hmehlan) +- [Steffen Möller](https://github.com/smoe) Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. From de0c007d70a3c4d97532a1918c31b8377b0e3462 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 16 Nov 2023 09:52:01 +0000 Subject: [PATCH 3/7] Update test data links --- conf/test.config | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/conf/test.config b/conf/test.config index d0430eacb..f9154ba31 100644 --- a/conf/test.config +++ b/conf/test.config @@ -21,19 +21,19 @@ params { // Input data - input = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/v3.10/samplesheet_test.csv" + input = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv" // Genome references - fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genome.fasta" - gtf = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genes.gtf.gz" - gff = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genes.gff.gz" - transcript_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/transcriptome.fasta" - additional_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/gfp.fa.gz" - - bbsplit_fasta_list = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/bbsplit_fasta_list.txt" - hisat2_index = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/hisat2.tar.gz" - salmon_index = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/salmon.tar.gz" - rsem_index = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/rsem.tar.gz" + fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genome.fasta" + gtf = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genes_with_empty_tid.gtf.gz" + gff = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genes.gff.gz" + transcript_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/transcriptome.fasta" + additional_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/gfp.fa.gz" + + bbsplit_fasta_list = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/bbsplit_fasta_list.txt" + hisat2_index = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/hisat2.tar.gz" + salmon_index = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/salmon.tar.gz" + rsem_index = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/rsem.tar.gz" // Other parameters skip_bbsplit = false From 14c29a660e2ed00e18245c0dfb6e07981f9b346a Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 16 Nov 2023 10:30:06 +0000 Subject: [PATCH 4/7] Add authors and licenses to scripts in bin/ where missing --- bin/deseq2_qc.r | 2 ++ bin/dupradar.r | 2 ++ bin/fasta2gtf.py | 3 +++ bin/fastq_dir_to_samplesheet.py | 2 ++ bin/filter_gtf.py | 3 +++ bin/mqc_features_stat.py | 2 ++ bin/summarizedexperiment.r | 2 ++ bin/tx2gene.py | 3 +++ bin/tximport.r | 2 ++ 9 files changed, 21 insertions(+) diff --git a/bin/deseq2_qc.r b/bin/deseq2_qc.r index d99bc7c2b..9397f5f30 100755 --- a/bin/deseq2_qc.r +++ b/bin/deseq2_qc.r @@ -1,5 +1,7 @@ #!/usr/bin/env Rscript +# Written by Harshil Patel and released under the MIT license. + ################################################ ################################################ ## REQUIREMENTS ## diff --git a/bin/dupradar.r b/bin/dupradar.r index daf5a5798..d58b0eee1 100755 --- a/bin/dupradar.r +++ b/bin/dupradar.r @@ -1,5 +1,7 @@ #!/usr/bin/env Rscript +# Written by Phil Ewels and released under the MIT license. + # Command line argument processing args = commandArgs(trailingOnly=TRUE) if (length(args) < 5) { diff --git a/bin/fasta2gtf.py b/bin/fasta2gtf.py index 052322b24..716ee06ce 100755 --- a/bin/fasta2gtf.py +++ b/bin/fasta2gtf.py @@ -1,4 +1,7 @@ #!/usr/bin/env python3 + +# Written by Pranathi Vemuri and released under the MIT license. + """ Read a custom fasta file and create a custom GTF containing each entry """ diff --git a/bin/fastq_dir_to_samplesheet.py b/bin/fastq_dir_to_samplesheet.py index 1eb3657c6..7ceebe525 100755 --- a/bin/fastq_dir_to_samplesheet.py +++ b/bin/fastq_dir_to_samplesheet.py @@ -1,5 +1,7 @@ #!/usr/bin/env python3 +# Written by Harshil Patel and released under the MIT license. + import os import sys import glob diff --git a/bin/filter_gtf.py b/bin/filter_gtf.py index 3d09bd859..265250627 100755 --- a/bin/filter_gtf.py +++ b/bin/filter_gtf.py @@ -1,4 +1,7 @@ #!/usr/bin/env python + +# Written by Olga Botvinnik with subsequent reworking by Jonathan Manning. Released under the MIT license. + import logging import argparse import re diff --git a/bin/mqc_features_stat.py b/bin/mqc_features_stat.py index 689a3f215..fa69b231c 100755 --- a/bin/mqc_features_stat.py +++ b/bin/mqc_features_stat.py @@ -1,5 +1,7 @@ #!/usr/bin/env python +# Written by Senthilkumar Panneerselvam and released under the MIT license. + import argparse import logging import os diff --git a/bin/summarizedexperiment.r b/bin/summarizedexperiment.r index d55101ecf..767d542c7 100755 --- a/bin/summarizedexperiment.r +++ b/bin/summarizedexperiment.r @@ -1,5 +1,7 @@ #!/usr/bin/env Rscript +# Written by Lorena Pantano and released under the MIT license. + library(SummarizedExperiment) ## Create SummarizedExperiment (se) object from counts diff --git a/bin/tx2gene.py b/bin/tx2gene.py index 0a418920e..8e0c1c6a5 100755 --- a/bin/tx2gene.py +++ b/bin/tx2gene.py @@ -1,4 +1,7 @@ #!/usr/bin/env python + +# Written by Lorena Pantano with subsequent reworking by Jonathan Manning. Released under the MIT license. + import logging import argparse import glob diff --git a/bin/tximport.r b/bin/tximport.r index e1bad7511..ee3d8b212 100755 --- a/bin/tximport.r +++ b/bin/tximport.r @@ -1,5 +1,7 @@ #!/usr/bin/env Rscript +# Written by Lorena Pantano and released under the MIT license. + library(SummarizedExperiment) library(tximport) From 6ff89c4b98b2a0bf1b386441bd2f3106cf5671dc Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 16 Nov 2023 10:37:26 +0000 Subject: [PATCH 5/7] Add release fix to changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ddeda910f..9eb25e856 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -37,7 +37,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [#1074](https://github.com/nf-core/rnaseq/issues/1074) - Enable quantification using StringTie AND a custom - [#1082](https://github.com/nf-core/rnaseq/issues/1082) - More informative error message for `filter_gtf_for_genes_in_genome.py` - [#1102](https://github.com/nf-core/rnaseq/issues/1102) - gene entries with empty transcript_id fields - Ensembl genome +- [#976](https://github.com/nf-core/rnaseq/issues/976) - Add author and licenses for all custom scripts ### Software dependencies From 2ea2ad1948b701c394987ae7690cbc8598778038 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 16 Nov 2023 12:05:44 +0100 Subject: [PATCH 6/7] [skip-ci] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9eb25e856..5df7b82b8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -33,11 +33,11 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1091](https://github.com/nf-core/rnaseq/pull/1091) - Reorganise parameters in schema for better usability - [PR #1106](https://github.com/nf-core/rnaseq/pull/1106) - Kallisto quantification - [PR #1107](https://github.com/nf-core/rnaseq/pull/1107) - Expand GTF filtering to remove rows with empty transcript ID when required, fix STAR GTF usage +- [#976](https://github.com/nf-core/rnaseq/issues/976) - Add author and licenses for all custom scripts - [#1050](https://github.com/nf-core/rnaseq/issues/1050) - Provide custom prefix/suffix for summary files to avoid overwriting - [#1074](https://github.com/nf-core/rnaseq/issues/1074) - Enable quantification using StringTie AND a custom - [#1082](https://github.com/nf-core/rnaseq/issues/1082) - More informative error message for `filter_gtf_for_genes_in_genome.py` - [#1102](https://github.com/nf-core/rnaseq/issues/1102) - gene entries with empty transcript_id fields -- [#976](https://github.com/nf-core/rnaseq/issues/976) - Add author and licenses for all custom scripts ### Software dependencies From 5070c5094d664c28044c0ff495c682732a24c1f9 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 16 Nov 2023 12:07:23 +0100 Subject: [PATCH 7/7] [skip-ci] Update bin/deseq2_qc.r --- bin/deseq2_qc.r | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/deseq2_qc.r b/bin/deseq2_qc.r index 9397f5f30..14bd48f70 100755 --- a/bin/deseq2_qc.r +++ b/bin/deseq2_qc.r @@ -1,6 +1,6 @@ #!/usr/bin/env Rscript -# Written by Harshil Patel and released under the MIT license. +# Written by Harshil Patel and Gavin Kelly and released under the MIT license. ################################################ ################################################