fix script paths

workflow/rules/consensus_peak_analysis.smk

@@ -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:

workflow/rules/igv_session.smk

@@ -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:

workflow/rules/ref.smk

@@ -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:

workflow/rules/trimming.smk

@@ -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"