tried replacing nanopolish with f5c, but will keep nanopolish bc idk …

…who f5c got screwed here
nf-core · Sep 18, 2024 · dd82756 · dd82756
1 parent 266d37c
commit dd82756
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Showing 5 changed files with 20 additions and 37 deletions.
diff --git a/modules/local/f5c_index_eventalign.nf b/modules/local/f5c_index_eventalign.nf
@@ -8,7 +8,7 @@ process F5C_INDEX_EVENTALIGN {
         'quay.io/biocontainers/f5c:1.5--h56e2c18_1' }"
 
     input:
-    tuple val(meta), path(genome), path(gtf), path(fastq), path(bam), path(bai), path(blow5)
+    tuple val(meta), path(genome), path(gtf), path(fastqgz), path(bam), path(bai)
 
     output:
     tuple val(meta), path(genome), path(gtf), path("*eventalign.txt"), path("*summary.txt"), emit: f5c_outputs
@@ -20,9 +20,14 @@ process F5C_INDEX_EVENTALIGN {
     script:
     sample_summary = "$meta.id" +"_summary.txt"
     sample_eventalign = "$meta.id" +"_eventalign.txt"
+    fastq="$meta.id"+".fastq"
+    fast5 = "$meta.fast5"
+    fastqi="$fastq"+"*"
     """
-    f5c index --slow5 $blow5 $fastq
-    f5c eventalign  --reads $fastq --bam $bam --genome $genome --slow5 $blow5 --scale-events --signal-index --summary $sample_summary --threads $task.cpus > $sample_eventalign
+    gunzip -c $fastqgz > $fastq
+    f5c index -d $fast5 $fastq
+    echo $fastqi
+    f5c eventalign --reads $fastq --bam $bam --genome $genome --scale-events --signal-index --rna --min-mapq 0 --min-recalib-events 1 --summary $sample_summary --threads $task.cpus > $sample_eventalign
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/local/gtf2bed.nf b/modules/local/gtf2bed.nf
@@ -7,7 +7,7 @@ process GTF2BED {
         'quay.io/biocontainers/perl:5.26.2' }"
 
     input:
-    tuple path(gtf), val(name)
+    tuple val(name), path(gtf)
 
     output:
     tuple path('*.bed'), val(name), emit: gtf_bed

diff --git a/modules/local/slow5tools_f2s_merge.nf b/modules/local/slow5tools_f2s_merge.nf
diff --git a/subworkflows/local/rna_modifications_xpore_m6anet.nf b/subworkflows/local/rna_modifications_xpore_m6anet.nf
@@ -2,22 +2,24 @@
  * RNA MODIFICATION DETECTION WITH XPORE AND M6ANET
  */
 
-include { NANOPOLISH_INDEX_EVENTALIGN } from '../../modules/local/nanopolish_index_eventalign'
+
+// include { F5C_INDEX_EVENTALIGN } from '../../modules/local/f5c_index_eventalign' // f5c works for my other pipeline, but idk how it got screwed here
+include { NANOPOLISH_INDEX_EVENTALIGN } from '../../modules/local/nanopolish_index_eventalign' // nanopolish does the job
 include { XPORE_DATAPREP        } from '../../modules/local/xpore_dataprep'
 include { XPORE_DIFFMOD         } from '../../modules/local/xpore_diffmod'
 include { M6ANET_DATAPREP        } from '../../modules/local/m6anet_dataprep'
 include { M6ANET_INFERENCE      } from '../../modules/local/m6anet_inference'
 
 workflow RNA_MODIFICATION_XPORE_M6ANET {
     take:
-    ch_nanopolish_bam_fast5
+    ch_bam_fast5
 
     main:
 
     /*
      * Align current signals to reference with Nanopolish
      */
-    NANOPOLISH_INDEX_EVENTALIGN { ch_nanopolish_bam_fast5 }
+    NANOPOLISH_INDEX_EVENTALIGN { ch_bam_fast5 }
     ch_nanopolish_outputs = NANOPOLISH_INDEX_EVENTALIGN.out.nanopolish_outputs
     nanopolish_version    = NANOPOLISH_INDEX_EVENTALIGN.out.versions
 

diff --git a/workflows/nanoseq.nf b/workflows/nanoseq.nf
@@ -126,6 +126,7 @@ include { GET_TEST_DATA         } from '../modules/local/get_test_data'
 include { GET_NANOLYSE_FASTA    } from '../modules/local/get_nanolyse_fasta'
 include { FAST5_TO_POD5         } from '../modules/local/fast5_to_pod5'
 include { DORADO                } from '../modules/local/dorado'
+include { GTF2BED               } from '../modules/local/gtf2bed'
 include { BAM_RENAME            } from '../modules/local/bam_rename'
 include { BAMBU                 } from '../modules/local/bambu'
 include { MULTIQC               } from '../modules/local/multiqc'
@@ -346,6 +347,11 @@ workflow NANOSEQ{
     ch_fai               = CUSTOM_GETCHROMSIZES.out.fai
     ch_software_versions = ch_software_versions.mix(CUSTOM_GETCHROMSIZES.out.versions.first().ifEmpty(null))
 
+    // will add the following in when nf-core/modules/minimap2/align supports junction bed input
+    //GTF2BED ( ch_chr_sizes )
+    //ch_gtf_bed = GTF2BED.out.gtf_bed
+    //gtf2bed_version = GTF2BED.out.versions
+
     ch_samtools_multiqc = Channel.empty()
     if (!params.skip_alignment) {