fix path

04_filter_samples/rules/dereplicate_samples.smk

@@ -11,4 +11,4 @@ rule dereplicate_samples:
     params:
         dmulti= lambda wildcards: dfMultiChecked[dfMultiChecked.demultiplex == wildcards.demultiplexs].to_dict('records')[0],        
     shell:
-        '''mkdir -p 01_dereplicated/{params.dmulti[projmarkrun]}; obiuniq -m sample {input} > {output} 2> {log}'''
\ No newline at end of file
+        '''mkdir -p ../results/04_filter_samples/01_dereplicated/{params.dmulti[projmarkrun]}; obiuniq -m sample {input} > {output} 2> {log}'''
\ No newline at end of file

04_filter_samples/rules/rm_internal_samples.smk

@@ -11,4 +11,4 @@ rule rm_internal_samples:
     log:
         '../logs/04_filter_samples/04_filtered/{demultiplexs}.log'
     shell:
-        '''if [[ -s {input} ]]; then mkdir -p 04_filtered/{params.dmulti[projmarkrun]}; obigrep -p "obiclean_internalcount == 0" {input} > {output} 2> {log} ; else touch {output} 2> {log} ; fi'''
+        '''if [[ -s {input} ]]; then mkdir -p ../results/04_filter_samples/04_filtered/{params.dmulti[projmarkrun]}; obigrep -p "obiclean_internalcount == 0" {input} > {output} 2> {log} ; else touch {output} 2> {log} ; fi'''