Trying to use libreads for id conversions.

CLIP/iCLIP.snakefile

@@ -541,14 +541,15 @@ rule feature_count_reads:
         err = OPJ(log_dir, "{trimmer}", "feature_count_reads", "{lib}_{rep}_{read_type}.err")
     shell:
         """
-        converter="/pasteur/entites/Mhe/Genomes/C_elegans/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes_id2name.pickle"
+        # converter="/pasteur/entites/Mhe/Genomes/C_elegans/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes_id2name.pickle"
         tmpdir=$(mktemp -dt "feature_{wildcards.lib}_{wildcards.rep}_{wildcards.read_type}_{wildcards.biotype}_{wildcards.orientation}.XXXXXXXXXX")
         cmd="featureCounts -a {params.annot} -o {output.counts} -t transcript -g "gene_id" -O -M --primary -s {params.stranded} --fracOverlap 0 --tmpDir ${{tmpdir}} {input.sorted_bam}"
         featureCounts -v 2> {log.log}
         echo ${{cmd}} 1>> {log.log}
         eval ${{cmd}} 1>> {log.log} 2> {log.err} || error_exit "featureCounts failed"
         rm -rf ${{tmpdir}}
-        cat {output.counts} | id2name.py ${{converter}} > {output.counts_converted}
+        cat {output.counts} | wormid2name > {output.counts_converted}
+        # cat {output.counts} | id2name.py ${{converter}} > {output.counts_converted}
         """
 
 

CLIP/requirements.txt

@@ -3,3 +3,5 @@ pandas
 libhts @ git+https://bioinfo_utils:DP-sqNot8AdsMek_KJiC@gitlab.pasteur.fr/bli/libhts.git
 libworkflows @ git+https://bioinfo_utils:tfuTQsSZWMtC5xXJNFJh@gitlab.pasteur.fr/bli/libworkflows.git
 snakemake_wrappers @ git+https://bioinfo_utils:Ues9rP1tyfzs1zs5BzpY@gitlab.pasteur.fr/bli/snakemake_wrappers.git
+# extra dependencies for some rules
+libcelegans @ git+https://bioinfo_utils:izoZHUvhFJU8689hqM5u@gitlab.pasteur.fr/bli/libcelegans.git

Degradome-seq/Degradome-seq.snakefile

@@ -227,7 +227,8 @@ rule feature_count_reads:
         echo ${{cmd}} 1>> {log.log}
         eval ${{cmd}} 1>> {log.log} 2> {log.err} || error_exit "featureCounts failed"
         rm -rf ${{tmpdir}}
-        cat {output.counts} | id2name.py {params.converter} > {output.counts_converted}
+        cat {output.counts} | wormid2name {params.converter} > {output.counts_converted}
+        # cat {output.counts} | id2name.py {params.converter} > {output.counts_converted}
         """
 
 

Degradome-seq/requirements.txt

@@ -2,3 +2,5 @@ numpy
 pandas
 snakemake_wrappers @ git+https://bioinfo_utils:Ues9rP1tyfzs1zs5BzpY@gitlab.pasteur.fr/bli/snakemake_wrappers.git
 libworkflows @ git+https://bioinfo_utils:tfuTQsSZWMtC5xXJNFJh@gitlab.pasteur.fr/bli/libworkflows.git
+# extra dependencies for some rules
+libcelegans @ git+https://bioinfo_utils:izoZHUvhFJU8689hqM5u@gitlab.pasteur.fr/bli/libcelegans.git

PRO-seq/PRO-seq.snakefile

@@ -703,7 +703,8 @@ rule feature_count_reads:
         echo ${{cmd}} 1>> {log.log}
         eval ${{cmd}} 1>> {log.log} 2> {log.err} || error_exit "featureCounts failed"
         rm -rf ${{tmpdir}}
-        cat {output.counts} | id2name.py {params.converter} > {output.counts_converted}
+        cat {output.counts} | wormid2name > {output.counts_converted}
+        # cat {output.counts} | id2name.py {params.converter} > {output.counts_converted}
         """
 
 

PRO-seq/requirements.txt

@@ -11,4 +11,5 @@ libhts @ git+https://bioinfo_utils:DP-sqNot8AdsMek_KJiC@gitlab.pasteur.fr/bli/li
 libworkflows @ git+https://bioinfo_utils:tfuTQsSZWMtC5xXJNFJh@gitlab.pasteur.fr/bli/libworkflows.git
 snakemake_wrappers @ git+https://bioinfo_utils:Ues9rP1tyfzs1zs5BzpY@gitlab.pasteur.fr/bli/snakemake_wrappers.git
 # extra dependencies for some rules
+libcelegans @ git+https://bioinfo_utils:izoZHUvhFJU8689hqM5u@gitlab.pasteur.fr/bli/libcelegans.git
 deeptools

RNA_Seq_Cecere/RNA-seq.snakefile

@@ -895,7 +895,8 @@ rule feature_count_reads:
         echo ${{cmd}} 1>> {log.log}
         eval ${{cmd}} 1>> {log.log} 2> {log.err} || error_exit "featureCounts failed"
         rm -rf ${{tmpdir}}
-        cat {output.counts} | id2name.py {params.converter} > {output.counts_converted}
+        cat {output.counts} | wormid2name > {output.counts_converted}
+        # cat {output.counts} | id2name.py {params.converter} > {output.counts_converted}
         """
 
 

RNA_Seq_Cecere/requirements.txt

@@ -11,3 +11,5 @@ libdeseq @ git+https://bioinfo_utils:uqiFbzWyBtzxYn7br82P@gitlab.pasteur.fr/bli/
 libhts @ git+https://bioinfo_utils:DP-sqNot8AdsMek_KJiC@gitlab.pasteur.fr/bli/libhts.git
 libworkflows @ git+https://bioinfo_utils:tfuTQsSZWMtC5xXJNFJh@gitlab.pasteur.fr/bli/libworkflows.git
 snakemake_wrappers @ git+https://bioinfo_utils:Ues9rP1tyfzs1zs5BzpY@gitlab.pasteur.fr/bli/snakemake_wrappers.git
+# extra dependencies for some rules
+libcelegans @ git+https://bioinfo_utils:izoZHUvhFJU8689hqM5u@gitlab.pasteur.fr/bli/libcelegans.git