update input set mapping

cidgoh · May 3, 2024 · 9c45d9d · 9c45d9d
1 parent 57c43bf
commit 9c45d9d
Show file tree

Hide file tree

Showing 4 changed files with 36 additions and 29 deletions.
diff --git a/nanopore_isolate_wgs.csv b/nanopore_isolate_wgs.csv
@@ -1,4 +1,4 @@
-sample,fastq_dir
-ERR7565110,/mnt/cidgoh-object-storage/hackathon/seqqc/isolate_wgs/nanopore/sra_split/ERR7565110/
-ERR7565112,/mnt/cidgoh-object-storage/hackathon/seqqc/isolate_wgs/nanopore/sra_split/ERR7565112/
-ERR7565113,/mnt/cidgoh-object-storage/hackathon/seqqc/isolate_wgs/nanopore/sra_split/ERR7565113/
+sample,fastq_1,fastq_2,fastq_dir,genome
+ERR7565110,,,/mnt/cidgoh-object-storage/hackathon/seqqc/isolate_wgs/nanopore/sra_split/ERR7565110/,
+ERR7565112,,,/mnt/cidgoh-object-storage/hackathon/seqqc/isolate_wgs/nanopore/sra_split/ERR7565112/,
+ERR7565113,,,/mnt/cidgoh-object-storage/hackathon/seqqc/isolate_wgs/nanopore/sra_split/ERR7565113/,
diff --git a/samplesheet_genome.csv b/samplesheet_genome.csv
@@ -1,3 +1,3 @@
-sample,genome
-GCA_010673125,/mnt/cidgoh-object-storage/hackathon/seqqc/genome_asm/GCA_010673125.1/GCA_010673125.1.fa
-GCA_010798115,/mnt/cidgoh-object-storage/hackathon/seqqc/genome_asm/GCA_010798115.1/GCA_010798115.1.fa
+sample,fastq_1,fastq_2,fastq_dir,genome
+GCA_010673125,,,,/mnt/cidgoh-object-storage/hackathon/seqqc/genome_asm/GCA_010673125.1/GCA_010673125.1.fa.gz
+GCA_010798115,,,,/mnt/cidgoh-object-storage/hackathon/seqqc/genome_asm/GCA_010798115.1/GCA_010798115.1.fa.gz
diff --git a/subworkflows/local/utils_nfcore_bacpaq_pipeline/main.nf b/subworkflows/local/utils_nfcore_bacpaq_pipeline/main.nf
@@ -81,29 +81,29 @@ workflow PIPELINE_INITIALISATION {
 
     Channel
         .fromSamplesheet("input")
-        .map {
-            meta, fastq_1, fastq_2, fastq_dir, genome ->
-
-            // map illumina data
-            if (fastq_1) {
-                if (!fastq_2) {
-                    return [ [ meta.id, single_end:true ], fastq_1 ]
-                } else {
-                    return [ [ meta.id, single_end:false ], fastq_1, fastq_2 ]
-                }
-            }
-
-            // map nanopore data
-            if (fastq_dir) {
-                return [ [ meta.id, single_end:true ], fastq_dir ]
-            }
-
-            // map nanopore data
-            if (genome) {
-                return [ [ meta.id, single_end:true ], genome ]
-            }
+        // .map {
+        //     meta, fastq_1, fastq_2, fastq_dir, genome ->
+
+        //     // map illumina data
+        //     if (fastq_1) {
+        //         if (!fastq_2) {
+        //             return [ [ id:meta.id, single_end: true ], fastq_1 ]
+        //         } else {
+        //             return [ [ id:meta.id, single_end: false ], fastq_1, fastq_2 ]
+        //         }
+        //     }
+
+        //     // map nanopore data
+        //     if (fastq_dir) {
+        //         return [ [ id:meta.id, single_end: true ], fastq_dir ]
+        //     }
+
+        //     // map nanopore data
+        //     if (genome) {
+        //         return [ [ id:meta.id, single_end: true ], genome ]
+        //     }
 
-        }
+        // }
         // .groupTuple()
         // .map {
         //     validateInputSamplesheet(it)

diff --git a/workflows/bacpaq.nf b/workflows/bacpaq.nf
@@ -28,7 +28,14 @@ workflow BACPAQ {
     multiqc_report = ''
 
     if (params.workflow == 'seqqc') {
+        // if (params.platform == 'illumina') {
+        //     ch_input = samplesheet
+        //         .map {
+        //             return [id:meta.id]
+        //         }
+        // }
         // SEQQC ()
+
         samplesheet.view()
     }
     else if (params.workflow == 'annotation') {