Merge pull request #1114 from nf-core/skip-ci]-update_contribs

Pre-release fixes for 3.13.0
nf-core · Nov 16, 2023 · 8b9ffe5 · 8b9ffe5
2 parents 7a04c5d + 5070c50
commit 8b9ffe5
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,10 +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/smoe)
 
 Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
 
@@ -31,11 +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
-  Ensembl genome
 
 ### Software dependencies
 

diff --git a/bin/deseq2_qc.r b/bin/deseq2_qc.r
@@ -1,5 +1,7 @@
 #!/usr/bin/env Rscript
 
+# Written by Harshil Patel and Gavin Kelly and released under the MIT license.
+
 ################################################
 ################################################
 ## REQUIREMENTS                               ##

diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -1,5 +1,7 @@
 #!/usr/bin/env Rscript
 
+# Written by Lorena Pantano and released under the MIT license.
+
 library(SummarizedExperiment)
 library(tximport)
 

diff --git 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