From fec62b5358ed1e85bb3e7dff32138769c13162fc Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Wed, 10 Jul 2024 13:29:06 +0200
Subject: [PATCH] Make local rule compatible with snakemake v5.
---
CLIP/iCLIP.snakefile | 2 ++
Degradome-seq/Degradome-seq.snakefile | 1 +
PRO-seq/PRO-seq.snakefile | 2 ++
RNA_Seq_Cecere/RNA-seq.snakefile | 2 ++
Ribo-seq/Ribo-seq.snakefile | 2 +-
requirements.txt | 2 +-
small_RNA-seq/small_RNA-seq.snakefile | 2 ++
snakemake_wrappers | 2 +-
8 files changed, 12 insertions(+), 3 deletions(-)
diff --git a/CLIP/iCLIP.snakefile b/CLIP/iCLIP.snakefile
index 40257c0..a85a7aa 100644
--- a/CLIP/iCLIP.snakefile
+++ b/CLIP/iCLIP.snakefile
@@ -274,6 +274,8 @@ counting = [
trimmer=TRIMMERS, lib=LIBS, read_type=["deduped"], biotype=["protein_coding"], orientation=ORIENTATIONS),
]
+localrules: all, link_raw_data
+
#TODO:
# - Plot histogram of read type counts at successive processing steps
# - Remap unmapped with less stringency to check if we are too stringent
diff --git a/Degradome-seq/Degradome-seq.snakefile b/Degradome-seq/Degradome-seq.snakefile
index 58889de..768516f 100644
--- a/Degradome-seq/Degradome-seq.snakefile
+++ b/Degradome-seq/Degradome-seq.snakefile
@@ -141,6 +141,7 @@ wildcard_constraints:
rep="\d+",
orientation="|".join(ORIENTATIONS),
+localrules: all, link_raw_data
rule all:
input:
diff --git a/PRO-seq/PRO-seq.snakefile b/PRO-seq/PRO-seq.snakefile
index 92bcc69..2b0aa19 100644
--- a/PRO-seq/PRO-seq.snakefile
+++ b/PRO-seq/PRO-seq.snakefile
@@ -353,6 +353,8 @@ else:
trimmer=TRIMMERS, counter=COUNTERS, biotype=COUNT_BIOTYPES,
orientation=ORIENTATIONS),
+localrules: all, link_raw_data
+
rule all:
"""This top rule is used to drive the whole workflow by taking as input its final products."""
input:
diff --git a/RNA_Seq_Cecere/RNA-seq.snakefile b/RNA_Seq_Cecere/RNA-seq.snakefile
index 9723776..b37e4ea 100644
--- a/RNA_Seq_Cecere/RNA-seq.snakefile
+++ b/RNA_Seq_Cecere/RNA-seq.snakefile
@@ -538,6 +538,8 @@ if len(REPS) > 1:
else:
warnings.warn("Replicates comparisons will not be run because there are not enough replicates.\n")
+localrules: all, link_raw_data
+
rule all:
input:
specific_input(aligner),
diff --git a/Ribo-seq/Ribo-seq.snakefile b/Ribo-seq/Ribo-seq.snakefile
index b1c0b2d..5b466a8 100644
--- a/Ribo-seq/Ribo-seq.snakefile
+++ b/Ribo-seq/Ribo-seq.snakefile
@@ -602,7 +602,7 @@ read_graphs = [
# TODO: check what can be done with "dt" (differential translation, a.k.a. translation efficiency difference)
-
+localrules: all, link_raw_data
rule all:
input:
diff --git a/requirements.txt b/requirements.txt
index dba25bd..d10b249 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -45,5 +45,5 @@ scikit-learn==0.23.2
scipy==1.5.2
seaborn==0.11.0
snakemake==5.24.2
-snakemake-wrappers @ git+https://gitlab.pasteur.fr/bli/snakemake_wrappers.git@dc5e29ac5bdbf70650865901927ba549ef4a565e
+snakemake-wrappers @ git+https://gitlab.pasteur.fr/bli/snakemake_wrappers.git@e78f5d0ce8487f8c226e1585b364789f47832e8f
tabulate==0.8.7
diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile
index a397d52..9666f4d 100644
--- a/small_RNA-seq/small_RNA-seq.snakefile
+++ b/small_RNA-seq/small_RNA-seq.snakefile
@@ -880,6 +880,8 @@ else:
fold_boxplots = [de_fold_boxplots, ip_fold_boxplots_by_contrast, ip_fold_boxplots]
+localrules: all, link_raw_data
+
rule all:
input:
expand(
diff --git a/snakemake_wrappers b/snakemake_wrappers
index dc5e29a..e78f5d0 160000
--- a/snakemake_wrappers
+++ b/snakemake_wrappers
@@ -1 +1 @@
-Subproject commit dc5e29ac5bdbf70650865901927ba549ef4a565e
+Subproject commit e78f5d0ce8487f8c226e1585b364789f47832e8f
--
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