From 4d116e28bd6cb379e7567c3a29a5099ee1252f78 Mon Sep 17 00:00:00 2001
From: rlegendr <rachel.legendre@pasteur.fr>
Date: Tue, 27 Jul 2021 11:44:29 +0200
Subject: [PATCH] update singularity
---
workflow/rules/bamCoverage.rules | 2 +-
workflow/rules/bed_to_gff.rules | 2 +-
workflow/rules/bowtie2_index.rules | 2 +-
workflow/rules/bowtie2_mapping.rules | 2 +-
workflow/rules/chipuanar.rules | 2 +-
workflow/rules/compute_idr.rules | 2 +-
workflow/rules/cutadapt.rules | 2 +-
workflow/rules/fastqc.rules | 2 +-
workflow/rules/feature_counts.rules | 3 +--
workflow/rules/intersectionApproach.rules | 2 +-
workflow/rules/macs2.rules | 2 +-
workflow/rules/mark_duplicates.rules | 2 +-
workflow/rules/multiqc.rules | 2 +-
workflow/rules/preIDR_PPR.rules | 2 +-
workflow/rules/preIDR_Pool.rules | 2 +-
workflow/rules/preIDR_SPR.rules | 2 +-
workflow/rules/remove_blacklist.rules | 2 +-
workflow/rules/select_peaks.rules | 2 +-
workflow/rules/spp.rules | 2 +-
workflow/rules/union_peaks.rules | 2 +-
20 files changed, 20 insertions(+), 21 deletions(-)
diff --git a/workflow/rules/bamCoverage.rules b/workflow/rules/bamCoverage.rules
index d812e23..30c61a8 100644
--- a/workflow/rules/bamCoverage.rules
+++ b/workflow/rules/bamCoverage.rules
@@ -29,7 +29,7 @@ rule bamCoverage:
output:
bamCoverage_output
singularity:
- "rnaflow.img"
+ "chipflow.img"
params:
options = bamCoverage_options
envmodules:
diff --git a/workflow/rules/bed_to_gff.rules b/workflow/rules/bed_to_gff.rules
index 46de44d..05ee544 100755
--- a/workflow/rules/bed_to_gff.rules
+++ b/workflow/rules/bed_to_gff.rules
@@ -30,7 +30,7 @@ rule bed_to_gff:
output:
temp(bed_to_gff_output)
singularity:
- "chipuana.img"
+ "chipflow.img"
shell:
"""
awk 'BEGIN{{OFS="\t"}} {{print $1"\tChIPflow\tpeak\t"$2+1"\t"$3+1"\t.\t.\t.\tgene_id \"$1"_"$2"_"$3}}' {input} > {output} 2> {log}
diff --git a/workflow/rules/bowtie2_index.rules b/workflow/rules/bowtie2_index.rules
index 40ddf77..8de9a44 100755
--- a/workflow/rules/bowtie2_index.rules
+++ b/workflow/rules/bowtie2_index.rules
@@ -28,7 +28,7 @@ rule bowtie2_index:
output:
bowtie2_index_output_done
singularity:
- "chipuana.img"
+ "chipflow.img"
params:
prefix = bowtie2_index_output_prefix
log:
diff --git a/workflow/rules/bowtie2_mapping.rules b/workflow/rules/bowtie2_mapping.rules
index 8b212f6..0694ad0 100755
--- a/workflow/rules/bowtie2_mapping.rules
+++ b/workflow/rules/bowtie2_mapping.rules
@@ -30,7 +30,7 @@ rule bowtie2_mapping:
sort = bowtie2_mapping_sort,
bam = temp(bowtie2_mapping_bam)
singularity:
- "chipuana.img"
+ "chipflow.img"
log:
err = bowtie2_mapping_logs_err,
out = bowtie2_mapping_logs_out
diff --git a/workflow/rules/chipuanar.rules b/workflow/rules/chipuanar.rules
index df49792..ae3c5dc 100755
--- a/workflow/rules/chipuanar.rules
+++ b/workflow/rules/chipuanar.rules
@@ -32,7 +32,7 @@ rule chipuanar:
log:
chipuanar_logs
singularity:
- "chipuana.img"
+ "chipflow.img"
shell:
"""
set +o pipefail
diff --git a/workflow/rules/compute_idr.rules b/workflow/rules/compute_idr.rules
index 73edb18..c9f149d 100755
--- a/workflow/rules/compute_idr.rules
+++ b/workflow/rules/compute_idr.rules
@@ -29,7 +29,7 @@ rule compute_idr:
idr = compute_idr_output,
peak = compute_idr_output_peak
singularity:
- "chipuana.img"
+ "chipflow.img"
log:
compute_idr_log
params:
diff --git a/workflow/rules/cutadapt.rules b/workflow/rules/cutadapt.rules
index 76b83a7..b0de6e0 100755
--- a/workflow/rules/cutadapt.rules
+++ b/workflow/rules/cutadapt.rules
@@ -36,7 +36,7 @@ rule cutadapt:
min = cutadapt_min,
qual = cutadapt_qual
singularity:
- "chipuana.img"
+ "chipflow.img"
threads: config['adapters']['threads']
log:
cutadapt_log
diff --git a/workflow/rules/fastqc.rules b/workflow/rules/fastqc.rules
index 267c26a..7a642f9 100755
--- a/workflow/rules/fastqc.rules
+++ b/workflow/rules/fastqc.rules
@@ -27,7 +27,7 @@ rule fastqc:
output:
touch(fastqc_output_done)
singularity:
- "chipuana.img"
+ "chipflow.img"
params:
wkdir = fastqc_wkdir,
kargs = config['fastqc']['options']
diff --git a/workflow/rules/feature_counts.rules b/workflow/rules/feature_counts.rules
index 23f82d5..e48fbeb 100755
--- a/workflow/rules/feature_counts.rules
+++ b/workflow/rules/feature_counts.rules
@@ -27,9 +27,8 @@ rule feature_counts:
gff = feature_counts_gff
output:
feature_counts_output_count
-
singularity:
- "chipuana.img"
+ "chipflow.img"
params:
mapp = feature_counts_options,
input = feature_counts_optional_input
diff --git a/workflow/rules/intersectionApproach.rules b/workflow/rules/intersectionApproach.rules
index a527fc1..329c96c 100755
--- a/workflow/rules/intersectionApproach.rules
+++ b/workflow/rules/intersectionApproach.rules
@@ -31,7 +31,7 @@ rule intersectionApproach:
output:
intersectionApproach_output
singularity:
- "chipuana.img"
+ "chipflow.img"
params:
overlap = intersectionApproach_overlap
shell:
diff --git a/workflow/rules/macs2.rules b/workflow/rules/macs2.rules
index a34b589..75e17db 100755
--- a/workflow/rules/macs2.rules
+++ b/workflow/rules/macs2.rules
@@ -40,7 +40,7 @@ rule macs2:
output:
macs2_output
singularity:
- "chipuana.img"
+ "chipflow.img"
shell:
"""
set +o pipefail
diff --git a/workflow/rules/mark_duplicates.rules b/workflow/rules/mark_duplicates.rules
index 35b1303..65154eb 100755
--- a/workflow/rules/mark_duplicates.rules
+++ b/workflow/rules/mark_duplicates.rules
@@ -29,7 +29,7 @@ rule mark_duplicates:
bam = mark_duplicates_output,
metrics = mark_duplicates_metrics
singularity:
- "chipuana.img"
+ "chipflow.img"
log:
out = mark_duplicates_log_std,
err = mark_duplicates_log_err
diff --git a/workflow/rules/multiqc.rules b/workflow/rules/multiqc.rules
index fc04a17..6448889 100755
--- a/workflow/rules/multiqc.rules
+++ b/workflow/rules/multiqc.rules
@@ -30,7 +30,7 @@ rule multiqc:
output:
multiqc_output
singularity:
- "chipuana.img"
+ "chipflow.img"
params:
inputdir = multiqc_input_dir,
options = multiqc_options,
diff --git a/workflow/rules/preIDR_PPR.rules b/workflow/rules/preIDR_PPR.rules
index d465a79..7ace16c 100755
--- a/workflow/rules/preIDR_PPR.rules
+++ b/workflow/rules/preIDR_PPR.rules
@@ -30,7 +30,7 @@ rule preIDR_PPR:
output:
preIDR_PPR_output
singularity:
- "chipuana.img"
+ "chipflow.img"
shell:
"""
set +o pipefail
diff --git a/workflow/rules/preIDR_Pool.rules b/workflow/rules/preIDR_Pool.rules
index c69e56d..6fcd05c 100755
--- a/workflow/rules/preIDR_Pool.rules
+++ b/workflow/rules/preIDR_Pool.rules
@@ -30,7 +30,7 @@ rule preIDR_pool:
output:
preIDR_pool_output
singularity:
- "chipuana.img"
+ "chipflow.img"
shell:
"""
set +o pipefail
diff --git a/workflow/rules/preIDR_SPR.rules b/workflow/rules/preIDR_SPR.rules
index 8c0fdf0..9e0f2d5 100755
--- a/workflow/rules/preIDR_SPR.rules
+++ b/workflow/rules/preIDR_SPR.rules
@@ -30,7 +30,7 @@ rule preIDR_SPR:
output:
preIDR_SPR_output
singularity:
- "chipuana.img"
+ "chipflow.img"
shell:
"""
set +o pipefail
diff --git a/workflow/rules/remove_blacklist.rules b/workflow/rules/remove_blacklist.rules
index 75facd2..79b4dcb 100755
--- a/workflow/rules/remove_blacklist.rules
+++ b/workflow/rules/remove_blacklist.rules
@@ -27,7 +27,7 @@ rule remove_blacklist:
output:
bam = remove_blacklist_output
singularity:
- "chipuana.img"
+ "chipflow.img"
log:
out = remove_blacklist_log_std,
err = remove_blacklist_log_err
diff --git a/workflow/rules/select_peaks.rules b/workflow/rules/select_peaks.rules
index d0f692a..e0f9a1f 100755
--- a/workflow/rules/select_peaks.rules
+++ b/workflow/rules/select_peaks.rules
@@ -32,7 +32,7 @@ rule select_peaks:
output:
select_peaks_output
singularity:
- "chipuana.img"
+ "chipflow.img"
shell:
"""
set +o pipefail
diff --git a/workflow/rules/spp.rules b/workflow/rules/spp.rules
index 4b55e58..73bcce3 100755
--- a/workflow/rules/spp.rules
+++ b/workflow/rules/spp.rules
@@ -31,7 +31,7 @@ rule spp:
params:
tmpdir = spp_tmpdir
singularity:
- "chipuana.img"
+ "chipflow.img"
log:
out = spp_log_std,
err = spp_log_err
diff --git a/workflow/rules/union_peaks.rules b/workflow/rules/union_peaks.rules
index 17b7093..a4c1e9c 100755
--- a/workflow/rules/union_peaks.rules
+++ b/workflow/rules/union_peaks.rules
@@ -29,7 +29,7 @@ rule union_peaks:
output:
union_peaks_output
singularity:
- "chipuana.img"
+ "chipflow.img"
shell:
"""
--
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