From 7a6edf428bf80fc02f43d8d66565cc6810977202 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 29 Mar 2023 14:08:22 +0200
Subject: [PATCH] fix csv parsing
---
data/sample.csv | 28 ++++++++++++++--------------
src/main.nf | 9 +++++----
2 files changed, 19 insertions(+), 18 deletions(-)
diff --git a/data/sample.csv b/data/sample.csv
index 091534e..4513a2c 100644
--- a/data/sample.csv
+++ b/data/sample.csv
@@ -1,14 +1,14 @@
-specie; sex; r1; r2
-mbelari; female; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/1_S1_L001_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/1_S1_L001_R2_001.fasta.gz
-mbelari; female; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/2_S2_L001_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/2_S2_L001_R2_001.fasta.gz
-mbelari; female; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/3_S3_L001_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/3_S3_L001_R2_001.fasta.gz
-mbelari; female; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/4_S4_L001_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/4_S4_L001_R2_001.fasta.gz
-mbelari; female; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/5_S5_L001_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/5_S5_L001_R2_001.fasta.gz
-mbelari; female; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/6_S6_L001_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/6_S6_L001_R2_001.fasta.gz
-mbelari; female; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/MRDR5_R1.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/MRDR5_R2.fasta.gz
-mbelari; male; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/JU2817_males_S11_L002_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/JU2817_males_S11_L002_R2_001.fasta.gz
-mbelari; male; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/MRDR6_R1.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/MRDR6_R2.fasta.gz
-mlongespiculosa; female; /scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_females/MRDR3_R1.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_females/MRDR3_R2.fasta.gz
-mlongespiculosa; male; /scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_males/MRDR4_R1.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_males/MRDR4_R1.fasta.gz
-mspiculigera; female; /scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_females/AF72-females_BIS_S8_L002_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_females/AF72-females_BIS_S8_L002_R2_001.fasta.gz
-mspiculigera; male; /scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_males/AF72-males_S7_L002_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_males/AF72-males_S7_L002_R2_001.fasta.gz
+specie,sex,r1,r2
+mbelari,female,/scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/1_S1_L001_R1_001.fasta.gz,/scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/1_S1_L001_R2_001.fasta.gz
+mbelari,female,/scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/2_S2_L001_R1_001.fasta.gz,/scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/2_S2_L001_R2_001.fasta.gz
+mbelari,female,/scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/3_S3_L001_R1_001.fasta.gz,/scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/3_S3_L001_R2_001.fasta.gz
+mbelari,female,/scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/4_S4_L001_R1_001.fasta.gz,/scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/4_S4_L001_R2_001.fasta.gz
+mbelari,female,/scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/5_S5_L001_R1_001.fasta.gz,/scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/5_S5_L001_R2_001.fasta.gz
+mbelari,female,/scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/6_S6_L001_R1_001.fasta.gz,/scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/6_S6_L001_R2_001.fasta.gz
+mbelari,female,/scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/MRDR5_R1.fasta.gz,/scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/MRDR5_R2.fasta.gz
+mbelari,male,/scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/JU2817_males_S11_L002_R1_001.fasta.gz,/scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/JU2817_males_S11_L002_R2_001.fasta.gz
+mbelari,male,/scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/MRDR6_R1.fasta.gz,/scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/MRDR6_R2.fasta.gz
+mlongespiculosa,female,/scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_females/MRDR3_R1.fasta.gz,/scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_females/MRDR3_R2.fasta.gz
+mlongespiculosa,male,/scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_males/MRDR4_R1.fasta.gz,/scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_males/MRDR4_R1.fasta.gz
+mspiculigera,female,/scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_females/AF72-females_BIS_S8_L002_R1_001.fasta.gz,/scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_females/AF72-females_BIS_S8_L002_R2_001.fasta.gz
+mspiculigera,male,/scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_males/AF72-males_S7_L002_R1_001.fasta.gz,/scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_males/AF72-males_S7_L002_R2_001.fasta.gz
diff --git a/src/main.nf b/src/main.nf
index a0194eb..9ebe5e7 100644
--- a/src/main.nf
+++ b/src/main.nf
@@ -10,13 +10,14 @@ include { FASTKMERS } from "./modules/fastkmers.nf"
Channel.fromPath( file(params.csv) )
.splitCsv(header: true)
.map{row ->
- fastq_r1 = file("${r1}")
- fastq_r2 = file("${r2}")
- meta = ['id': ${fastq_r1.simpleName},, 'specie': ${specie}, 'sex': ${sex}]
+ fastq_r1 = file("${row.r1}")
+ fastq_r2 = file("${row.r2}")
+ meta = ['id': fastq_r1.simpleName, 'specie': row.specie, 'sex': row.sex]
+ println(row)
[meta, [fastq_r1, fastq_r2]]
}
.set{ fastq }
workflow {
- FASTLMERS(fastq)
+ FASTKMERS(fastq)
}
--
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