From 0eb879a8d2a40a3d0b3ff765e0fdfdca62df126d Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Wed, 30 Oct 2019 16:02:10 +0100
Subject: [PATCH] Fix path to snakemake wrappers.
---
CLIP/iCLIP.snakefile | 6 +++---
Degradome-seq/Degradome-seq.snakefile | 8 ++++----
PRO-seq/PRO-seq.snakefile | 10 +++++-----
RNA_Seq_Cecere/RNA-seq.snakefile | 14 +++++++-------
Ribo-seq/Ribo-seq.snakefile | 4 ++--
small_RNA-seq/small_RNA-seq.snakefile | 6 +++---
6 files changed, 24 insertions(+), 24 deletions(-)
diff --git a/CLIP/iCLIP.snakefile b/CLIP/iCLIP.snakefile
index b56f154..c63d677 100644
--- a/CLIP/iCLIP.snakefile
+++ b/CLIP/iCLIP.snakefile
@@ -427,7 +427,7 @@ rule map_on_genome:
err = OPJ(log_dir, "{trimmer}", aligner, "map_{read_type}_on_genome", "{lib}_{rep}.err"),
threads: 12
wrapper:
- f"file://{wrappers_dir}/map_on_genome"
+ f"file://{wrappers_dir[0]}/map_on_genome"
rule remap_on_genome:
@@ -455,7 +455,7 @@ rule remap_on_genome:
err = OPJ(log_dir, "{trimmer}", aligner, "remap_{read_type}_unmapped_on_genome", "{lib}_{rep}.err"),
threads: 12
wrapper:
- f"file://{wrappers_dir}/map_on_genome"
+ f"file://{wrappers_dir[0]}/map_on_genome"
rule sam2indexedbam:
@@ -474,7 +474,7 @@ rule sam2indexedbam:
resources:
mem_mb=4100
wrapper:
- f"file://{wrappers_dir}/sam2indexedbam"
+ f"file://{wrappers_dir[0]}/sam2indexedbam"
rule compute_mapping_stats:
diff --git a/Degradome-seq/Degradome-seq.snakefile b/Degradome-seq/Degradome-seq.snakefile
index f91c701..bed3a3a 100644
--- a/Degradome-seq/Degradome-seq.snakefile
+++ b/Degradome-seq/Degradome-seq.snakefile
@@ -170,7 +170,7 @@ rule map_on_genome:
threads:
4
wrapper:
- f"file://{wrappers_dir}/map_on_genome"
+ f"file://{wrappers_dir[0]}/map_on_genome"
rule sam2indexedbam:
@@ -189,7 +189,7 @@ rule sam2indexedbam:
resources:
mem_mb=4100
wrapper:
- f"file://{wrappers_dir}/sam2indexedbam"
+ f"file://{wrappers_dir[0]}/sam2indexedbam"
def biotype2annot(wildcards):
@@ -396,7 +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:
- f"file://{wrappers_dir}/compute_RPK"
+ f"file://{wrappers_dir[0]}/compute_RPK"
# Compute TPM using total number of mappers divided by genome length
@@ -418,7 +418,7 @@ rule compute_TPM:
# tpm = 1000000 * rpk / rpk.sum()
# tpm.to_csv(output.tpm_file, sep="\t")
wrapper:
- f"file://{wrappers_dir}/compute_TPM"
+ f"file://{wrappers_dir[0]}/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 b1d73f0..1e70b4e 100644
--- a/PRO-seq/PRO-seq.snakefile
+++ b/PRO-seq/PRO-seq.snakefile
@@ -491,7 +491,7 @@ rule map_on_genome:
# eval ${{cmd}} 1>> {log.log} 2>> {log.err}
# """
wrapper:
- f"file://{wrappers_dir}/map_on_genome"
+ f"file://{wrappers_dir[0]}/map_on_genome"
rule sam2indexedbam:
@@ -510,7 +510,7 @@ rule sam2indexedbam:
resources:
mem_mb=4100
wrapper:
- f"file://{wrappers_dir}/sam2indexedbam"
+ f"file://{wrappers_dir[0]}/sam2indexedbam"
rule fuse_bams:
@@ -655,7 +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:
- f"file://{wrappers_dir}/htseq_count_reads"
+ f"file://{wrappers_dir[0]}/htseq_count_reads"
def parse_htseq_counts(counts_filename):
@@ -964,7 +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:
- f"file://{wrappers_dir}/compute_RPK"
+ f"file://{wrappers_dir[0]}/compute_RPK"
rule compute_sum_million_RPK:
@@ -995,7 +995,7 @@ rule compute_TPM:
# tpm = 1000000 * rpk / rpk.sum()
# tpm.to_csv(output.tpm_file, sep="\t")
wrapper:
- f"file://{wrappers_dir}/compute_TPM"
+ f"file://{wrappers_dir[0]}/compute_TPM"
@wc_applied
diff --git a/RNA_Seq_Cecere/RNA-seq.snakefile b/RNA_Seq_Cecere/RNA-seq.snakefile
index 534c174..b749bdb 100644
--- a/RNA_Seq_Cecere/RNA-seq.snakefile
+++ b/RNA_Seq_Cecere/RNA-seq.snakefile
@@ -566,7 +566,7 @@ rule map_on_genome:
#shell:
# mapping_command(aligner)
wrapper:
- f"file://{wrappers_dir}/map_on_genome"
+ f"file://{wrappers_dir[0]}/map_on_genome"
rule extract_nomap_polyU:
@@ -619,7 +619,7 @@ rule remap_on_genome:
#shell:
# mapping_command(aligner)
wrapper:
- f"file://{wrappers_dir}/map_on_genome"
+ f"file://{wrappers_dir[0]}/map_on_genome"
def source_sam(wildcards):
@@ -659,7 +659,7 @@ rule sam2indexedbam:
threads:
8
wrapper:
- f"file://{wrappers_dir}/sam2indexedbam"
+ f"file://{wrappers_dir[0]}/sam2indexedbam"
rule compute_mapping_stats:
@@ -838,7 +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:
-# f"file://{wrappers_dir}/htseq_count_reads"
+# f"file://{wrappers_dir[0]}/htseq_count_reads"
def source_sorted_bam(wildcards):
@@ -984,7 +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:
-# f"file://{wrappers_dir}/intersect_count_reads"
+# f"file://{wrappers_dir[0]}/intersect_count_reads"
rule summarize_counts:
@@ -1108,7 +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:
- f"file://{wrappers_dir}/compute_RPK"
+ f"file://{wrappers_dir[0]}/compute_RPK"
rule compute_sum_million_RPK:
@@ -1143,7 +1143,7 @@ rule compute_TPM:
# tpm = 1000000 * rpk / rpk.sum()
# tpm.to_csv(output.tpm_file, sep="\t")
wrapper:
- f"file://{wrappers_dir}/compute_TPM"
+ f"file://{wrappers_dir[0]}/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 8d45d15..9a17428 100644
--- a/Ribo-seq/Ribo-seq.snakefile
+++ b/Ribo-seq/Ribo-seq.snakefile
@@ -752,7 +752,7 @@ rule map_on_genome:
threads:
4
wrapper:
- f"file://{wrappers_dir}/map_on_genome"
+ f"file://{wrappers_dir[0]}/map_on_genome"
def source_sam(wildcards):
@@ -786,7 +786,7 @@ rule sam2indexedbam:
resources:
mem_mb=4100
wrapper:
- f"file://{wrappers_dir}/sam2indexedbam"
+ f"file://{wrappers_dir[0]}/sam2indexedbam"
rule compute_mapping_stats:
diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile
index 8e8c88c..d7f5e34 100644
--- a/small_RNA-seq/small_RNA-seq.snakefile
+++ b/small_RNA-seq/small_RNA-seq.snakefile
@@ -1013,7 +1013,7 @@ rule map_on_genome:
resources:
mem_mb=700
wrapper:
- f"file://{wrappers_dir}/map_on_genome"
+ f"file://{wrappers_dir[0]}/map_on_genome"
rule extract_nomap_siRNAs:
@@ -1066,7 +1066,7 @@ rule remap_on_genome:
resources:
mem_mb=700
wrapper:
- f"file://{wrappers_dir}/map_on_genome"
+ f"file://{wrappers_dir[0]}/map_on_genome"
def source_sam(wildcards):
@@ -1101,7 +1101,7 @@ rule sam2indexedbam:
resources:
mem_mb=4100
wrapper:
- f"file://{wrappers_dir}/sam2indexedbam"
+ f"file://{wrappers_dir[0]}/sam2indexedbam"
rule compute_coverage:
--
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