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Merge pull request #1114 from nf-core/skip-ci]-update_contribs
Pre-release fixes for 3.13.0
2 parents 7a04c5d + 5070c50 commit 8b9ffe5

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‎CHANGELOG.md

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Special thanks to the following for their contributions to the release:
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- [Adam Talbot](https://github.com/adamrtalbot)
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- [hmehlan](https://github.com/hmehlan)
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- [Jonathan Manning](https://github.com/pinin4fjords)
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- [Júlia Mir Pedrol](https://github.com/mirpedrol)
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- [Matthias Zepper](https://github.com/MatthiasZepper)
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- [Maxime Garcia](https://github.com/maxulysse)
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- [Steffen Möller](https://github.com/smoe)
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Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
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- [PR #1091](https://github.com/nf-core/rnaseq/pull/1091) - Reorganise parameters in schema for better usability
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- [PR #1106](https://github.com/nf-core/rnaseq/pull/1106) - Kallisto quantification
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- [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
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- [#976](https://github.com/nf-core/rnaseq/issues/976) - Add author and licenses for all custom scripts
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- [#1050](https://github.com/nf-core/rnaseq/issues/1050) - Provide custom prefix/suffix for summary files to avoid overwriting
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- [#1074](https://github.com/nf-core/rnaseq/issues/1074) - Enable quantification using StringTie AND a custom
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- [#1082](https://github.com/nf-core/rnaseq/issues/1082) - More informative error message for `filter_gtf_for_genes_in_genome.py`
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- [#1102](https://github.com/nf-core/rnaseq/issues/1102) - gene entries with empty transcript_id fields
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Ensembl genome
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### Software dependencies
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‎bin/deseq2_qc.r

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#!/usr/bin/env Rscript
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# Written by Harshil Patel and Gavin Kelly and released under the MIT license.
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################################################
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################################################
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## REQUIREMENTS ##

‎bin/dupradar.r

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#!/usr/bin/env Rscript
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# Written by Phil Ewels and released under the MIT license.
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# Command line argument processing
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args = commandArgs(trailingOnly=TRUE)
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if (length(args) < 5) {

‎bin/fasta2gtf.py

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#!/usr/bin/env python3
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# Written by Pranathi Vemuri and released under the MIT license.
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"""
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Read a custom fasta file and create a custom GTF containing each entry
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"""

‎bin/fastq_dir_to_samplesheet.py

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#!/usr/bin/env python3
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# Written by Harshil Patel and released under the MIT license.
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import os
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import sys
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import glob

‎bin/filter_gtf.py

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#!/usr/bin/env python
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# Written by Olga Botvinnik with subsequent reworking by Jonathan Manning. Released under the MIT license.
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import logging
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import argparse
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import re

‎bin/mqc_features_stat.py

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#!/usr/bin/env python
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# Written by Senthilkumar Panneerselvam and released under the MIT license.
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import argparse
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import logging
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import os

‎bin/summarizedexperiment.r

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#!/usr/bin/env Rscript
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# Written by Lorena Pantano and released under the MIT license.
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library(SummarizedExperiment)
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## Create SummarizedExperiment (se) object from counts

‎bin/tx2gene.py

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#!/usr/bin/env python
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# Written by Lorena Pantano with subsequent reworking by Jonathan Manning. Released under the MIT license.
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import logging
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import argparse
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import glob

‎bin/tximport.r

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#!/usr/bin/env Rscript
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# Written by Lorena Pantano and released under the MIT license.
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library(SummarizedExperiment)
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library(tximport)
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‎conf/test.config

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// Input data
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input = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/v3.10/samplesheet_test.csv"
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input = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv"
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// Genome references
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fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genome.fasta"
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gtf = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genes.gtf.gz"
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gff = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genes.gff.gz"
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transcript_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/transcriptome.fasta"
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additional_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/gfp.fa.gz"
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bbsplit_fasta_list = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/bbsplit_fasta_list.txt"
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hisat2_index = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/hisat2.tar.gz"
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salmon_index = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/salmon.tar.gz"
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rsem_index = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/rsem.tar.gz"
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fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genome.fasta"
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gtf = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genes_with_empty_tid.gtf.gz"
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gff = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genes.gff.gz"
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transcript_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/transcriptome.fasta"
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additional_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/gfp.fa.gz"
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bbsplit_fasta_list = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/bbsplit_fasta_list.txt"
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hisat2_index = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/hisat2.tar.gz"
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salmon_index = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/salmon.tar.gz"
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rsem_index = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/rsem.tar.gz"
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// Other parameters
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skip_bbsplit = false

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