fix csv parsing

data/sample.csv

-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

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)
 }