diff --git a/CLIP/iCLIP.snakefile b/CLIP/iCLIP.snakefile
index dc5e72ef8b5e5921c8937c8ce9271f509cb2e04c..b56f1546587c98699873869210a20cd486f2757a 100644
--- a/CLIP/iCLIP.snakefile
+++ b/CLIP/iCLIP.snakefile
@@ -32,6 +32,7 @@ from libworkflows import last_lines, ensure_relative, SHELL_FUNCTIONS, warn_cont
from libworkflows import feature_orientation2stranded
from libworkflows import sum_by_family, read_feature_counts, sum_feature_counts
from smincludes import rules as irules
+from smwrappers import wrappers_dir
# Define functions to be used in shell portions
shell.prefix(SHELL_FUNCTIONS)
@@ -426,7 +427,7 @@ rule map_on_genome:
err = OPJ(log_dir, "{trimmer}", aligner, "map_{read_type}_on_genome", "{lib}_{rep}.err"),
threads: 12
wrapper:
- "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/map_on_genome"
+ f"file://{wrappers_dir}/map_on_genome"
rule remap_on_genome:
@@ -454,7 +455,7 @@ rule remap_on_genome:
err = OPJ(log_dir, "{trimmer}", aligner, "remap_{read_type}_unmapped_on_genome", "{lib}_{rep}.err"),
threads: 12
wrapper:
- "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/map_on_genome"
+ f"file://{wrappers_dir}/map_on_genome"
rule sam2indexedbam:
@@ -473,7 +474,7 @@ rule sam2indexedbam:
resources:
mem_mb=4100
wrapper:
- "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/sam2indexedbam"
+ f"file://{wrappers_dir}/sam2indexedbam"
rule compute_mapping_stats:
diff --git a/Degradome-seq/Degradome-seq.snakefile b/Degradome-seq/Degradome-seq.snakefile
index d16a60ebc46d34f93552e0a9ac5fd192f8771b51..f91c701b5e8d57102f8f9b83ec3efe9528e9eb7b 100644
--- a/Degradome-seq/Degradome-seq.snakefile
+++ b/Degradome-seq/Degradome-seq.snakefile
@@ -20,6 +20,7 @@ from functools import reduce
from operator import or_ as union
from smincludes import rules as irules
+from smwrappers import wrappers_dir
from libworkflows import (
cleanup_and_backup,
column_converter,
@@ -169,7 +170,7 @@ rule map_on_genome:
threads:
4
wrapper:
- "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/map_on_genome"
+ f"file://{wrappers_dir}/map_on_genome"
rule sam2indexedbam:
@@ -188,7 +189,7 @@ rule sam2indexedbam:
resources:
mem_mb=4100
wrapper:
- "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/sam2indexedbam"
+ f"file://{wrappers_dir}/sam2indexedbam"
def biotype2annot(wildcards):
@@ -395,7 +396,7 @@ rule compute_RPK:
# rpk = 1000 * counts_data.loc[common].div(feature_lengths.loc[common]["union_exon_len"], axis="index")
# rpk.to_csv(output.rpk_file, sep="\t")
wrapper:
- "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/compute_RPK"
+ f"file://{wrappers_dir}/compute_RPK"
# Compute TPM using total number of mappers divided by genome length
@@ -417,7 +418,7 @@ rule compute_TPM:
# tpm = 1000000 * rpk / rpk.sum()
# tpm.to_csv(output.tpm_file, sep="\t")
wrapper:
- "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/compute_TPM"
+ f"file://{wrappers_dir}/compute_TPM"
# TODO: Is it better to compute the mean and then the fold of the means?
diff --git a/PRO-seq/PRO-seq.snakefile b/PRO-seq/PRO-seq.snakefile
index 7bf0fe83f5d0535bf1ee356a23a8858b397bf5f6..b1d73f0428049baa1a4837f56cd33a3fdcd95f2a 100644
--- a/PRO-seq/PRO-seq.snakefile
+++ b/PRO-seq/PRO-seq.snakefile
@@ -70,6 +70,7 @@ from libworkflows import sum_by_family
from libworkflows import read_htseq_counts, sum_htseq_counts
from libworkflows import read_feature_counts, sum_feature_counts
from smincludes import rules as irules
+from smwrappers import wrappers_dir
alignment_settings = {"bowtie2": ""}
@@ -490,7 +491,7 @@ rule map_on_genome:
# eval ${{cmd}} 1>> {log.log} 2>> {log.err}
# """
wrapper:
- "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/map_on_genome"
+ f"file://{wrappers_dir}/map_on_genome"
rule sam2indexedbam:
@@ -509,7 +510,7 @@ rule sam2indexedbam:
resources:
mem_mb=4100
wrapper:
- "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/sam2indexedbam"
+ f"file://{wrappers_dir}/sam2indexedbam"
rule fuse_bams:
@@ -654,7 +655,7 @@ rule htseq_count_reads:
log = OPJ(log_dir, "{trimmer}", "htseq_count_reads", "{lib}_{rep}_{biotype}_{orientation}.log"),
err = OPJ(log_dir, "{trimmer}", "htseq_count_reads", "{lib}_{rep}_{biotype}_{orientation}.err")
wrapper:
- "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/htseq_count_reads"
+ f"file://{wrappers_dir}/htseq_count_reads"
def parse_htseq_counts(counts_filename):
@@ -963,7 +964,7 @@ rule compute_RPK:
# rpk = 1000 * counts_data.loc[common].div(feature_lengths.loc[common]["union_exon_len"], axis="index")
# rpk.to_csv(output.rpk_file, sep="\t")
wrapper:
- "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/compute_RPK"
+ f"file://{wrappers_dir}/compute_RPK"
rule compute_sum_million_RPK:
@@ -994,7 +995,7 @@ rule compute_TPM:
# tpm = 1000000 * rpk / rpk.sum()
# tpm.to_csv(output.tpm_file, sep="\t")
wrapper:
- "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/compute_TPM"
+ f"file://{wrappers_dir}/compute_TPM"
@wc_applied
diff --git a/RNA_Seq_Cecere/RNA-seq.snakefile b/RNA_Seq_Cecere/RNA-seq.snakefile
index 9f32a1f9f7e53cd6d2d8426d96c56b7e04de4d0b..534c17404a4541ea43eb46f6942096520be74322 100644
--- a/RNA_Seq_Cecere/RNA-seq.snakefile
+++ b/RNA_Seq_Cecere/RNA-seq.snakefile
@@ -107,6 +107,7 @@ from libworkflows import read_htseq_counts, sum_htseq_counts
from libworkflows import read_intersect_counts, sum_intersect_counts
from libworkflows import read_feature_counts, sum_feature_counts
from smincludes import rules as irules
+from smwrappers import wrappers_dir
alignment_settings = {"bowtie2": "", "hisat2": "", "crac": "-k 20 --stranded --use-x-in-cigar"}
@@ -565,7 +566,7 @@ rule map_on_genome:
#shell:
# mapping_command(aligner)
wrapper:
- "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/map_on_genome"
+ f"file://{wrappers_dir}/map_on_genome"
rule extract_nomap_polyU:
@@ -618,7 +619,7 @@ rule remap_on_genome:
#shell:
# mapping_command(aligner)
wrapper:
- "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/map_on_genome"
+ f"file://{wrappers_dir}/map_on_genome"
def source_sam(wildcards):
@@ -658,7 +659,7 @@ rule sam2indexedbam:
threads:
8
wrapper:
- "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/sam2indexedbam"
+ f"file://{wrappers_dir}/sam2indexedbam"
rule compute_mapping_stats:
@@ -837,7 +838,7 @@ def biotype2annot(wildcards):
# log = OPJ(log_dir, "htseq_count_reads", "{lib}_{rep}_{biotype}_{orientation}.log"),
# err = OPJ(log_dir, "htseq_count_reads", "{lib}_{rep}_{biotype}_{orientation}.err"),
# wrapper:
-# "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/htseq_count_reads"
+# f"file://{wrappers_dir}/htseq_count_reads"
def source_sorted_bam(wildcards):
@@ -983,7 +984,7 @@ rule feature_count_reads:
# err = OPJ(log_dir, "intersect_count_reads", "{lib}_{rep}_{biotype}_{orientation}.err"),
# threads: 4 # to limit memory usage, actually
# wrapper:
-# "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/intersect_count_reads"
+# f"file://{wrappers_dir}/intersect_count_reads"
rule summarize_counts:
@@ -1107,7 +1108,7 @@ rule compute_RPK:
# rpk = 1000 * counts_data.loc[common].div(feature_lengths.loc[common]["union_exon_len"], axis="index")
# rpk.to_csv(output.rpk_file, sep="\t")
wrapper:
- "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/compute_RPK"
+ f"file://{wrappers_dir}/compute_RPK"
rule compute_sum_million_RPK:
@@ -1142,7 +1143,7 @@ rule compute_TPM:
# tpm = 1000000 * rpk / rpk.sum()
# tpm.to_csv(output.tpm_file, sep="\t")
wrapper:
- "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/compute_TPM"
+ f"file://{wrappers_dir}/compute_TPM"
# Useful to compute translation efficiency in the Ribo-seq pipeline
diff --git a/Ribo-seq/Ribo-seq.snakefile b/Ribo-seq/Ribo-seq.snakefile
index 4b0b89c6f4f00a481d9b5851a262646446ddb2d6..8d45d1555a4772a4e0332c88035d49fa87a0e15b 100644
--- a/Ribo-seq/Ribo-seq.snakefile
+++ b/Ribo-seq/Ribo-seq.snakefile
@@ -139,6 +139,7 @@ from libworkflows import get_chrom_sizes, column_converter, make_id_list_getter
from libworkflows import read_int_from_file, strip_split, file_len, last_lines, save_plot, SHELL_FUNCTIONS
from libworkflows import sum_by_family, read_feature_counts, sum_feature_counts, sum_htseq_counts, warn_context
from smincludes import rules as irules
+from smwrappers import wrappers_dir
strip = str.strip
alignment_settings = {"bowtie2": "-L 6 -i S,1,0.8 -N 0"}
@@ -751,7 +752,7 @@ rule map_on_genome:
threads:
4
wrapper:
- "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/map_on_genome"
+ f"file://{wrappers_dir}/map_on_genome"
def source_sam(wildcards):
@@ -785,7 +786,7 @@ rule sam2indexedbam:
resources:
mem_mb=4100
wrapper:
- "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/sam2indexedbam"
+ f"file://{wrappers_dir}/sam2indexedbam"
rule compute_mapping_stats:
diff --git a/snakemake_wrappers b/snakemake_wrappers
index e8105a64fe84747d407b19ca8db69bd54b66cb2e..6bbed10e5ab6f8b195a0a562376fbc5bc487cb06 160000
--- a/snakemake_wrappers
+++ b/snakemake_wrappers
@@ -1 +1 @@
-Subproject commit e8105a64fe84747d407b19ca8db69bd54b66cb2e
+Subproject commit 6bbed10e5ab6f8b195a0a562376fbc5bc487cb06