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Commit b9bcf9ba authored by BIOPZ-Iborra de Toledo Paula's avatar BIOPZ-Iborra de Toledo Paula
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updated

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......@@ -3,18 +3,18 @@
### Inputs
##############################################################################
# List of "organism/prefix"
organism: ["Homo_sapiens/GRCh38"]
organism: ["ORGANISM/PREFIX"]
#################### PARAMETERS SPECIFIC TO ORGANISM #########################
Homo_sapiens/GRCh38: {
genome_url: "ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz",
gtf_url: "ftp://ftp.ensembl.org/pub/release-99/gtf/homo_sapiens/Homo_sapiens.GRCh38.99.gtf.gz",
mirna_url: "ftp://mirbase.org/pub/mirbase/CURRENT/genomes/hsa.gff3",
ORGANISM/PREFIX: {
genome_url: " ##### ",
gtf_url: " ##### ",
mirna_url: " ##### ",
# Dictionary chromosome/contig name mappings between UCSC <-> Ensembl
# Other organisms available at: https://github.com/dpryan79/ChromosomeMappings
map_chr_url: "https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/GRCh38_UCSC2ensembl.txt",
map_chr_url: " ##### ",
# Chromosome names mapping parameters:
column: 1, #column number from input file where to change chromosome name
delimiter: "TAB" #delimiter of the input file
......
......@@ -35,12 +35,11 @@ snakemake \
--printshellcmds \
--snakefile="../workflow/Snakefile" \
--configfile="config.yaml" \
--cluster-config="cluster.json" \
--jobscript="../scripts/jobscript.sh" \
--use-singularity \
--singularity-args "--bind ${PWD},${PWD}/../" \
--cores=4 \
--rerun-incomplete \
--configfile config.yaml \
--verbose
# Snakemake report
......
#!/bin/bash
# Tear down test environment
# Tear down environment
cleanup () {
rc=$?
rm -rf .snakemake/
......
......@@ -3,8 +3,6 @@
# Tear down test environment
cleanup () {
rc=$?
#rm -rf .snakemake
#rm -rf logs/
cd $user_dir
echo "Exit status: $rc"
}
......
......@@ -3,8 +3,6 @@
# Tear down test environment
cleanup () {
rc=$?
#rm -rf .snakemake
#rm -rf logs/
cd $user_dir
echo "Exit status: $rc"
}
......
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