Updated- cleaned

Author: JD2112

.DS_Store

@@ -1,4 +1,5 @@
 work/
 .nextflow*
-
-.DS_Store
+.DS_Store
+.nextflow/
+pipeline_info/

.gitignore

@@ -1,7 +1,7 @@
 params {
     // Input/Output options
     sample_sheet    = null // "$projectDir/Sample_sheet_twist.csv"
-    genome_fasta    = null // /mnt/SD2/Jyotirmoys/JD/Scripts/MyScripts/JDCo/DNAm/DNAm-NF2/data/reference_genome/hg38/hg38.fa
+    genome_fasta    = null // 
     bismark_index   = false  // Set to false to generate index, or provide path to existing index
     diff_meth_method = 'edger' // or 'methylkit'
     design_file     = null

.nextflow/cache/7ea84b5f-9d51-46a6-9e6b-b94449abad2a/db/000003.log

@@ -2,8 +2,8 @@ process BISMARK_GENOME_PREPARATION {
     tag "$genome"
     label 'process_high'
 
-    conda "bioconda::bismark=0.23.0"
-    container "quay.io/biocontainers/bismark:0.23.0--hdfd78af_1"
+    // conda "bioconda::bismark=0.23.0"
+    // container "quay.io/biocontainers/bismark:0.23.0--hdfd78af_1"
 
     input:
     path genome
@@ -27,61 +27,6 @@ process BISMARK_GENOME_PREPARATION {
     """
 }
 
-// process BISMARK_ALIGN {
-//     tag "$meta.id"
-//     label 'process_high'
-
-//     conda "bioconda::bismark=0.23.0"
-//     container "quay.io/biocontainers/bismark:0.23.0--hdfd78af_1"
-
-//     input:
-//     tuple val(meta), path(reads)
-//     path index
-
-//     output:
-//     tuple val(meta), path("*.bam"), emit: bam
-//     tuple val(meta), path("*_report.txt"), emit: report
-//     path "versions.yml", emit: versions
-
-//     script:
-//     def args = task.ext.args ?: ''
-//     def prefix = task.ext.prefix ?: "${meta.id}"
-//     """
-//     echo "Copying index directory..."
-//     mkdir -p copied_index
-//     cp -rL $index/* ./copied_index/
-
-//     echo "Contents of copied index directory:"
-//     ls -lR ./copied_index
-
-//     echo "Searching for genome file:"
-//     genome_file=\$(find ./copied_index -name "*.fa" -o -name "*.fasta" | head -n 1)
-    
-//     if [ -z "\$genome_file" ]; then
-//         echo "No genome file found in index directory"
-//         exit 1
-//     else
-//         echo "Found genome file: \$genome_file"
-//         echo "First few lines of genome file:"
-//         head -n 5 "\$genome_file"
-//     fi
-
-//     bismark --genome ./copied_index \\
-//         $args \\
-//         -1 ${reads[0]} \\
-//         -2 ${reads[1]} \\
-//         --basename $prefix
-
-//     mv ${prefix}_pe.bam ${prefix}.bam
-
-//     cat <<-END_VERSIONS > versions.yml
-//     "${task.process}":
-//         bismark: \$( bismark --version | sed -e "s/Bismark Version: v//g" )
-//     END_VERSIONS
-//     """
-// }
-
-// In modules/bismark.nf
 process BISMARK_ALIGN {
     tag "$meta.id"
     label 'process_bismark_align'
@@ -108,13 +53,6 @@ process BISMARK_ALIGN {
     def reads_command = single_end ? "-s $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
 
     """
-    echo "Debug: Starting BISMARK_ALIGN for ${meta.id}"
-    echo "Debug: Single-end: ${single_end}"
-    echo "Debug: Reads: ${reads}"
-    echo "Debug: Index: ${index}"
-    echo "Debug: Prefix: ${prefix}"
-    echo "Debug: CPUs: ${task.cpus}"
-    echo "Debug: Memory: ${task.memory}"
 
     bismark \\
         $args \\
@@ -124,9 +62,6 @@ process BISMARK_ALIGN {
         -p ${task.cpus} \\
         $reads_command
 
-    echo "Debug: BISMARK_ALIGN completed for ${meta.id}"
-
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         bismark: \$(bismark --version | sed -e "s/Bismark Version: v//g")