From 689cb3e2d96cec872eddaa3e4bb2736f561a88c8 Mon Sep 17 00:00:00 2001
From: xgrand <xavier.grand@ens-lyon.fr>
Date: Mon, 13 Sep 2021 16:56:51 +0200
Subject: [PATCH] =?UTF-8?q?d=C3=A9marrage=20modif=20peak=20calling,=20pris?=
=?UTF-8?q?e=20en=20charge=20des=20IP=20et=20Ctrl.?=
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Content-Type: text/plain; charset=UTF-8
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---
src/chipster.nf | 14 +-------------
src/test.nf | 16 ++++++++++++++++
2 files changed, 17 insertions(+), 13 deletions(-)
create mode 100644 src/test.nf
diff --git a/src/chipster.nf b/src/chipster.nf
index b900127f..931935e3 100755
--- a/src/chipster.nf
+++ b/src/chipster.nf
@@ -152,9 +152,6 @@ include { index_bam } from "./nf_modules/samtools/main.nf"
include { bam_to_bigwig } from "./nf_modules/deeptools/main.nf"
include { chipseq_bam2BG } from "./nf_modules/deeptools/main.nf"
include { peak_calling_bg } from "./nf_modules/macs3/main.nf"
-include { bam_to_bed } from "./nf_modules/bedtools/main.nf"
-include { bed_slop } from "./nf_modules/bedtools/main.nf"
-include { bed_to_bedGraph } from "./nf_modules/bedtools/main.nf"
/*
****************************************************************
@@ -184,7 +181,7 @@ workflow {
// mapping preprocessed reads
mapping_fastq(index_fasta.out.index.collect(), fastp_default.out.fastq)
- /*if (!params.idxgenome) {
+ /*if (params.idxgenome == "") {
index_fasta(genome_file)
mapping_fastq(index_fasta.out.index.collect(), fastp_default.out.fastq)
} else {
@@ -207,15 +204,6 @@ workflow {
// Chipseq Bam 2 bigwig file with reads extends
chipseq_bam2BG(index_bam.out.bam_idx)
- // From Bam to Bed
- // bam_to_bed(sort_bam.out.bam)
-
- // Extension of reads with bedtools slop
- // bed_slop(bam_to_bed.out.bed, genome_sizes.collect())
-
- // From bed to bedgraph
- // bed_to_bedGraph(bed_slop.out, genome_sizes.collect())
-
// peak calling using MACS3 Prend des bed ou des bam en entrée...
// peak_calling_bg()
}
\ No newline at end of file
diff --git a/src/test.nf b/src/test.nf
new file mode 100644
index 00000000..be6c7083
--- /dev/null
+++ b/src/test.nf
@@ -0,0 +1,16 @@
+nextflow.enable.dsl=2
+
+
+Channel
+ .from([[1, "fastq1.fq"], [2, "fastq2.fq"], [3, "fastq3.fq"], [4, "fastq4.fq"]])
+ .set{ fastq_files }
+
+Channel
+ .from([[1, "test"], [2, "test"], [3, "ctrl"], [4, "ctrl"]])
+ .set { sample_names }
+
+
+// fastq_files.join(sample_names).map{it -> [file(it[1]).baseName, it[1], it[2]]}.view()
+fastq_files.join(sample_names).set{ vals }
+
+vals.combine(vals).filter { it -> (it[2] != it[5]) && (it[2] == "test") }.view()
\ No newline at end of file
--
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