updated a function name from hicexplorer3 (#596)

* Added a function to write the tools which have been used for each pipeline along with hteir versions. * renamed the findResSite function, since it has been renamed in hicexplorer3 * removed an extra line of code * updated the bash scripts to restrict mode for some functions in hicexplorer shared rule * updated more bash comments to restricted mode Co-authored-by: Leily Rabbani <[email protected]>
maxplanck-ie · Mar 13, 2020 · b883235 · b883235
1 parent bcaaacf
commit b883235
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/snakePipes/shared/rules/hicexplorer.snakefile b/snakePipes/shared/rules/hicexplorer.snakefile
@@ -11,7 +11,7 @@ rule get_restrictionSite:
         err = "log/get_restrictionSite.err"
     conda: CONDA_HIC_ENV
     shell:
-        "findRestSite -f {input} --searchPattern {params.res_seq} -o {output} > {log.out} 2> {log.err}"
+        "hicFindRestSite -f {input} --searchPattern {params.res_seq} -o {output} > {log.out} 2> {log.err}"
 
 
 # Map
@@ -110,7 +110,7 @@ rule merge_matrices:
          err = "HiC_matrices/logs/hicSumMatrices_{group}_"+matrixFile_suffix+".err"
       conda: CONDA_HIC_ENV
       shell:
-          "hicSumMatrices -m {input} -o {output.matrix} > {log.out} &> {log.err}"
+          "hicSumMatrices -m {input} -o {output.matrix} > {log.out} 2> {log.err}"
 
 ## Merge the bins if asked
 rule merge_bins:
@@ -138,7 +138,7 @@ rule diagnostic_plot:
         chr = lambda wildcards: " --chromosomes " + chromosomes if chromosomes else ""
     conda: CONDA_HIC_ENV
     shell:
-       "hicCorrectMatrix diagnostic_plot -m {input} -o {output.plot} {params.chr} &> {output.mad} "
+       "hicCorrectMatrix diagnostic_plot -m {input} -o {output.plot} {params.chr} 2> {output.mad} "
 
 
 # Compute MAD score thresholds
@@ -182,7 +182,7 @@ else:
          conda: CONDA_HIC_ENV
          shell:
              "hicCorrectMatrix correct --correctionMethod KR "
-             " {params.chr} -m {input.matrix} -o {output} > {log.out}"
+             " {params.chr} -m {input.matrix} -o {output} 2> {log.out}"
 
 ## Call TADs
 rule call_tads: