Verified Commit df14705a authored by Aurélien Ginolhac's avatar Aurélien Ginolhac 🚴
Browse files

fix script paths

parent e351c0bb
......@@ -82,7 +82,7 @@ rule plot_peak_intersect:
log:
"logs/macs2_merged_expand/plots/{antibody}.consensus_{peak}-peaks.boolean.intersect.plot.log"
shell:
"Rscript ../workflow/scripts/plot_peak_intersect.R -i {input} -o {output} 2> {log}"
"Rscript workflow/scripts/plot_peak_intersect.R -i {input} -o {output} 2> {log}"
rule create_consensus_igv:
input:
......
......@@ -20,7 +20,7 @@ rule igv_files_to_session:
log:
"logs/igv/igv_session_to_file.log"
shell:
" ../workflow/scripts/igv_files_to_session.py {output} {input.igv} ../../{input.fasta} {params} 2> {log}"
" workflow/scripts/igv_files_to_session.py {output} {input.igv} ../../{input.fasta} {params} 2> {log}"
# remove paths for igv session to download from report.zip
rule igv_report_cleanup:
......@@ -44,7 +44,7 @@ rule igv_files_to_report:
log:
"logs/igv/igv_files_to_report.log"
shell:
" ../workflow/scripts/igv_files_to_session.py {output} {input.igv} $(basename {input.fasta}) {params} 2> {log}"
" workflow/scripts/igv_files_to_session.py {output} {input.igv} $(basename {input.fasta}) {params} 2> {log}"
rule collect_igv_report_session_files:
input:
......
......@@ -63,7 +63,7 @@ rule gtf2bed:
conda:
"../envs/perl.yaml"
shell:
"../workflow/scripts/gtf2bed {input} > {output} 2> {log}"
"workflow/scripts/gtf2bed {input} > {output} 2> {log}"
rule genome_faidx:
input:
......
......@@ -12,8 +12,6 @@ rule trimming_pe:
params:
adapter = config["trimming"]["pe"],
others = config["trimming"]["others"]
container:
"docker://ginolhac/snake-rna-seq:0.4"
threads: config["trimming"]["threads"]
log:
"logs/trimming/{sample}-{unit}.pe.log"
......@@ -35,8 +33,6 @@ rule trimming_se:
params:
adapter = config["trimming"]["se"],
others = config["trimming"]["others"]
container:
"docker://ginolhac/snake-rna-seq:0.4"
threads: config["trimming"]["threads"]
log:
"logs/trimming/{sample}-{unit}.se.log"
......
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