Merge branch 'master' of github.com:eQTL-Catalogue/rnaseq

eQTL-Catalogue · Apr 27, 2022 · 04487a4 · 04487a4
2 parents ce3bc56 + f6a775a
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diff --git a/README.md b/README.md
@@ -20,7 +20,7 @@ The schema shown below represents the high level structure of the pipeline.
 # ![nfcore/rnaseq](docs/images/pipeline_high_level_schema.svg)
 
 ### Credits
-This pipeline is highly influenced by much earlier version of [nf-core/rnaseq](https://github.com/nf-core/rnaseq) pipeline which was originally written for use at the [National Genomics Infrastructure](https://portal.scilifelab.se/genomics/), part of [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden, by Phil Ewels ([@ewels](https://github.com/ewels)) and Rickard Hammarén ([@Hammarn](https://github.com/Hammarn)).
+This pipeline is highly influenced by much earlier version of the [nf-core/rnaseq](https://github.com/nf-core/rnaseq) pipeline which was originally written for use at the [National Genomics Infrastructure](https://portal.scilifelab.se/genomics/), part of [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden, by Phil Ewels ([@ewels](https://github.com/ewels)) and Rickard Hammarén ([@Hammarn](https://github.com/Hammarn)).
 
 New quantification methods (exon expression, transcript usage, transcriptional event usage and intron-splicing usage) are added by [Alasoo Lab](https://kauralasoo.github.io/) within the OpenTargets [eQTL Catalogue](https://www.ebi.ac.uk/eqtl/) project. Please cite [eQTL Catalogue paper](https://www.nature.com/articles/s41588-021-00924-w) if this resource have been used for your research. 
 [https://doi.org/10.1038/s41588-021-00924-w](https://doi.org/10.1038/s41588-021-00924-w)

diff --git a/conf/test.config b/conf/test.config
@@ -9,7 +9,7 @@
 
 params {
  // Input data
- readPathsFile = "data/read_pathes_GEUVADIS_GBR_20samples.tsv"
+ readPathsFile = "data/read_paths_GEUVADIS_GBR20.tsv"
  // Genome references
  unstranded = true
  outdir = "results/test_GEUVADIS_20samples"

diff --git a/data/read_pathes_GEUVADIS_GBR_20samples.tsv → data/read_paths_GEUVADIS_GBR20.tsv b/data/read_pathes_GEUVADIS_GBR_20samples.tsv → data/read_paths_GEUVADIS_GBR20.tsv
diff --git a/data/read_paths_GEUVADIS_GBR20_singleEnd.tsv b/data/read_paths_GEUVADIS_GBR20_singleEnd.tsv
@@ -0,0 +1,20 @@
+ERR188028 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR188/ERR188028/ERR188028_1.fastq.gz
+ERR188035 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR188/ERR188035/ERR188035_1.fastq.gz
+ERR188036 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR188/ERR188036/ERR188036_1.fastq.gz
+ERR188040 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR188/ERR188040/ERR188040_1.fastq.gz
+ERR188041 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR188/ERR188041/ERR188041_1.fastq.gz
+ERR188053 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR188/ERR188053/ERR188053_1.fastq.gz
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+ERR188065 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR188/ERR188065/ERR188065_1.fastq.gz
+ERR188070 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR188/ERR188070/ERR188070_1.fastq.gz
+ERR188071 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR188/ERR188071/ERR188071_1.fastq.gz
+ERR188073 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR188/ERR188073/ERR188073_1.fastq.gz
+ERR188080 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR188/ERR188080/ERR188080_1.fastq.gz
+ERR188082 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR188/ERR188082/ERR188082_1.fastq.gz
+ERR188087 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR188/ERR188087/ERR188087_1.fastq.gz
+ERR188091 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR188/ERR188091/ERR188091_1.fastq.gz
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+ERR188111 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR188/ERR188111/ERR188111_1.fastq.gz
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+ERR188116 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR188/ERR188116/ERR188116_1.fastq.gz