From 4a42bfff139b86a61ede25150a62d62b39ea6abf Mon Sep 17 00:00:00 2001
From: WardDeb <ward@deboutte.be>
Date: Fri, 9 Aug 2024 13:46:24 +0200
Subject: [PATCH] properly dispose of log directives

---
 snakePipes/shared/rules/CSAW.multiComp.snakefile  | 6 ------
 snakePipes/shared/rules/CSAW.singleComp.snakefile | 4 ----
 snakePipes/shared/rules/hicexplorer.snakefile     | 2 +-
 3 files changed, 1 insertion(+), 11 deletions(-)

diff --git a/snakePipes/shared/rules/CSAW.multiComp.snakefile b/snakePipes/shared/rules/CSAW.multiComp.snakefile
index 431679e75..1d9945a9a 100644
--- a/snakePipes/shared/rules/CSAW.multiComp.snakefile
+++ b/snakePipes/shared/rules/CSAW.multiComp.snakefile
@@ -123,8 +123,6 @@ rule calc_matrix_log2r_CSAW:
     threads: 8
     conda: CONDA_SHARED_ENV
     shell: """
-        touch {log.out}
-        touch {log.err}
         if [[ -s {params.bed_in} ]]; then
             computeMatrix scale-regions -S {input.bigwigs} -R {params.bed_in} -m 1000 -b 200 -a 200 -o {output.matrix} -p {threads}
         fi
@@ -141,8 +139,6 @@ rule plot_heatmap_log2r_CSAW:
         smpl_label = lambda wildcards: ' '.join(reordered_dict[wildcards.compGroup].keys())
     conda: CONDA_SHARED_ENV
     shell: """
-        touch {log.out}
-        touch {log.err}
         if [[ -s {input.matrix} ]]; then
             plotHeatmap --matrixFile {input.matrix} \
                         --outFileSortedRegions {output.sorted_regions} \
@@ -167,8 +163,6 @@ rule calc_matrix_cov_CSAW:
     threads: 8
     conda: CONDA_SHARED_ENV
     shell: """
-        touch {log.out}
-        touch {log.err}
         if [[ -s {params.bed_in} ]]; then
             computeMatrix scale-regions -S {input.bigwigs} -R {params.bed_in} \
             -m 1000 -b 200 -a 200 -o {output.matrix} -p {threads}
diff --git a/snakePipes/shared/rules/CSAW.singleComp.snakefile b/snakePipes/shared/rules/CSAW.singleComp.snakefile
index b63b429a7..52f38656c 100644
--- a/snakePipes/shared/rules/CSAW.singleComp.snakefile
+++ b/snakePipes/shared/rules/CSAW.singleComp.snakefile
@@ -148,8 +148,6 @@ rule calc_matrix_cov_CSAW:
     threads: 8
     conda: CONDA_SHARED_ENV
     shell: """
-        touch {log.out}
-        touch {log.err}
         if [[ -s {params.bed_in} ]]; then
             computeMatrix scale-regions -S {input.bigwigs} -R {params.bed_in} \
             -m 1000 -b 200 -a 200 -o {output.matrix} -p {threads}
@@ -167,8 +165,6 @@ rule plot_heatmap_cov_CSAW:
         smpl_label=' '.join(reordered_dict.keys())
     conda: CONDA_SHARED_ENV
     shell: """
-        touch {log.out}
-        touch {log.err}
         if [[ -s {input.matrix} ]]; then
             plotHeatmap --matrixFile {input.matrix} \
                     --outFileSortedRegions {output.sorted_regions} \
diff --git a/snakePipes/shared/rules/hicexplorer.snakefile b/snakePipes/shared/rules/hicexplorer.snakefile
index 8bc9e56cb..345e281b6 100644
--- a/snakePipes/shared/rules/hicexplorer.snakefile
+++ b/snakePipes/shared/rules/hicexplorer.snakefile
@@ -38,7 +38,7 @@ rule map_fastq_single_end:
     threads: lambda wildcards: 15 if 15<max_thread else max_thread
     conda: CONDA_HIC_ENV
     shell:
-        "echo 'mapping {input}' > {log.out} && "
+        "echo 'mapping {input}' && "
         "{params.aligner_cmd} -A1 -B4  -E50 -L0 "
         "-t {threads} {params.aligner_index} {input} | "
         "samtools view -Shb - > {output.out}"