From 5e5da78e409d804c714c44d900f9b63bb2c0a1f0 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Tue, 4 Dec 2018 17:55:18 +0100
Subject: [PATCH] No PCA when only one library.
Also updated one gene list name.
---
PRO-seq/PRO-seq.snakefile | 21 +++++++++++++++------
1 file changed, 15 insertions(+), 6 deletions(-)
diff --git a/PRO-seq/PRO-seq.snakefile b/PRO-seq/PRO-seq.snakefile
index 7adb766..fba5319 100644
--- a/PRO-seq/PRO-seq.snakefile
+++ b/PRO-seq/PRO-seq.snakefile
@@ -169,7 +169,7 @@ ID_LISTS = [
"germline_specific",
"histone",
"spermatogenic_Ortiz_2014", "oogenic_Ortiz_2014",
- "piRNA_dependent_prot_si_down4_WR_RT_top200", "piRNA_dependent_prot_si_down4",
+ "piRNA_dependent_prot_si_down4_WR_RT_top200", "piRNA_dependent_prot_si_22G_down4",
"csr1_prot_si_supertargets_common"]
annot_dir = config["annot_dir"]
gene_lists_dir = "/pasteur/entites/Mhe/bli/Gene_lists"
@@ -287,6 +287,14 @@ wildcard_constraints:
# Define functions to be used in shell portions
shell.prefix(SHELL_FUNCTIONS)
+if len(CONDITIONS) < 2:
+ pca_figs = []
+else:
+ pca_figs = expand(OPJ(
+ output_dir, "{trimmer}", "figures", aligner, "{counter}",
+ "{biotype}_{orientation}_PCA.pdf"),
+ trimmer=TRIMMERS, counter=COUNTERS, biotype=COUNT_BIOTYPES,
+ orientation=ORIENTATIONS),
rule all:
"""This top rule is used to drive the whole workflow by taking as input its final products."""
@@ -306,11 +314,12 @@ rule all:
"deseq2", "{contrast}", "{orientation}_{biotype}", "counts_and_res.txt"),
trimmer=TRIMMERS, counter=COUNTERS, contrast=CONTRASTS,
orientation=ORIENTATIONS, biotype=DE_BIOTYPES),
- expand(OPJ(
- output_dir, "{trimmer}", "figures", aligner, "{counter}",
- "{biotype}_{orientation}_PCA.pdf"),
- trimmer=TRIMMERS, counter=COUNTERS, biotype=COUNT_BIOTYPES,
- orientation=ORIENTATIONS),
+ pca_figs,
+ #expand(OPJ(
+ # output_dir, "{trimmer}", "figures", aligner, "{counter}",
+ # "{biotype}_{orientation}_PCA.pdf"),
+ # trimmer=TRIMMERS, counter=COUNTERS, biotype=COUNT_BIOTYPES,
+ # orientation=ORIENTATIONS),
#expand(OPJ(output_dir, "{trimmer}", aligner, "mapped_C_elegans", "{counter}", "all_on_C_elegans", "alltypes_{orientation}_counts.txt"), trimmer=TRIMMERS, counter=COUNTERS, orientation=["all"]),
#expand(expand(OPJ(output_dir, "{{trimmer}}", aligner, "mapped_C_elegans", "{{counter}}", "{lib}_{rep}_on_C_elegans", "{{biotype}}_{{orientation}}_counts.txt"), filtered_product, lib=LIBS, rep=REPS), trimmer=TRIMMERS, counter=COUNTERS, biotype=COUNT_BIOTYPES, orientation=["all"]),
expand(expand(OPJ(
--
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