diff --git a/CLIP/iCLIP.snakefile b/CLIP/iCLIP.snakefile index b56f1546587c98699873869210a20cd486f2757a..b52fb5f050a1bcf770e147e25b04a436e767d673 100644 --- a/CLIP/iCLIP.snakefile +++ b/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} """ diff --git a/CLIP/requirements.txt b/CLIP/requirements.txt index f128eabd3d63dd742abcaba55ce3220e46bdaa3e..fc0e8a5db68dceddb383de27575c4b394b4855b6 100644 --- a/CLIP/requirements.txt +++ b/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 diff --git a/Degradome-seq/Degradome-seq.snakefile b/Degradome-seq/Degradome-seq.snakefile index f91c701b5e8d57102f8f9b83ec3efe9528e9eb7b..91effc614166aa31bd2e52574c830c69093f7be5 100644 --- a/Degradome-seq/Degradome-seq.snakefile +++ b/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} """ diff --git a/Degradome-seq/requirements.txt b/Degradome-seq/requirements.txt index 336115a66c58dff38f5f28a912ec9fc7755db558..38c60ce5450cad3ed6e5b2bea676ec602f258e04 100644 --- a/Degradome-seq/requirements.txt +++ b/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 diff --git a/PRO-seq/PRO-seq.snakefile b/PRO-seq/PRO-seq.snakefile index b1d73f0428049baa1a4837f56cd33a3fdcd95f2a..8e12e5bcf22100c0d2e1b7a7390970a69ea64fcc 100644 --- a/PRO-seq/PRO-seq.snakefile +++ b/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} """ diff --git a/PRO-seq/requirements.txt b/PRO-seq/requirements.txt index 958e2dfd4a6a436af4460fa4ce51d28489cb4688..4fa1c4c48ac87de773b059f86acc82baaa70bc00 100644 --- a/PRO-seq/requirements.txt +++ b/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 diff --git a/RNA_Seq_Cecere/RNA-seq.snakefile b/RNA_Seq_Cecere/RNA-seq.snakefile index 534c17404a4541ea43eb46f6942096520be74322..6f9b41901e0529193442477022395b851b89fbd3 100644 --- a/RNA_Seq_Cecere/RNA-seq.snakefile +++ b/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} """ diff --git a/RNA_Seq_Cecere/requirements.txt b/RNA_Seq_Cecere/requirements.txt index c63dab2220e233d14c414be4b26b56a53949a872..9258ec060c1756360996c7425eccee0fe04a681c 100644 --- a/RNA_Seq_Cecere/requirements.txt +++ b/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