slight changes, will leave tests to home PC

Author: number-25

assets/Dockerfile assets/Dockerfile_bambuassets/Dockerfile renamed to assets/Dockerfile_bambu

@@ -9,7 +9,6 @@
 
 process {
 
-    // TODO nf-core: Check the defaults for all processes
     cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
     memory = { check_max( 6.GB * task.attempt, 'memory' ) }
     time   = { check_max( 4.h  * task.attempt, 'time'   ) }
@@ -19,7 +18,6 @@ process {
     maxErrors     = '-1'
 
     // Process-specific resource requirements
-    // TODO nf-core: Customise requirements for specific processes.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
         cpus   = { check_max( 1                  , 'cpus'    ) }

assets/Dockerfile_bugged assets/Dockerfile_bambu_2assets/Dockerfile_bugged renamed to assets/Dockerfile_bambu_2

@@ -19,8 +19,7 @@ params {
     // Input data for full size test
     // nf-core: Give any required params for the test so that command line flags are not needed
     input  = /test/samplesheets/samplesheet_testfull_dRNA.csv'
-    //input_path =
-    'https://github.com/nf-core/test-datasets/blob/nanoseq/fastq/demultiplexed/quantification/bambu/MCF7_directRNA_replicate4.fastq.gz'
+    //input_path = 'https://github.com/nf-core/test-datasets/blob/nanoseq/fastq/demultiplexed/quantification/bambu/MCF7_directRNA_replicate4.fastq.gz'
 
     // Limit resources so that this can run on GitHub Actions
     //max_cpus                        = 2
@@ -69,11 +68,11 @@ params {
     extra_isoquant_options          = null
     run_stringtie                   = true
     extra_stringtie_options         = null
-    skip_jaffal                     = true
-    skip_jaffal_download            = true
-    skip_sqanti_all                 = true
+    skip_jaffal                     = false
+    skip_jaffal_download            = false
     skip_gffcompare                 = false
     extra_gffcompare_options        = null
+    skip_sqanti_all                 = true
     skip_sqanti_qc                  = true
     sqanti_qc_reference             = 'human'
     sqanti_qc_cage                  = true

conf/local_arch.config

@@ -172,10 +172,6 @@ workflow DIRECTRNA{
     // INPUT_CHECK
     INPUT_CHECK ( ch_input )
         .set { ch_sample }
-    // playing around with channel transformations
-    ///ch_sample
-    ///.map { it -> [ it[0], it[1] ] } // take sample, replicate, reads
-    ///.set { ch_fastq }
 
     // QC of fastq files
     /// MODULES: NANOQ & SEQUALI
@@ -196,7 +192,7 @@ workflow DIRECTRNA{
 
     // Prepare the reference files
     /// SUBWORKFLOW: PREPARE_REFERENCE
-   /* if (!params.skip_prepare_reference) {
+    if (!params.skip_prepare_reference) {
         PREPARE_REFERENCE (
             params.genome_fasta,
             params.genome_fasta_index,
@@ -223,8 +219,11 @@ workflow DIRECTRNA{
         ch_transcriptome_fasta          = PREPARE_REFERENCE.out.transcriptome_fasta
         ch_annotation_gtf               = PREPARE_REFERENCE.out.annotation_gtf
         ch_jaffal_reference_dir         = PREPARE_REFERENCE.out.jaffal_reference
+        // Combine genome fasta with genome fasta index into single channel -
+        // some software expect both files in a single path/channel
+        ch_genome_fasta_with_index = ch_genome_fasta.combine(ch_genome_fasta_index)
 
-        // initialize sqanti qc references
+   /*     // initialize sqanti qc references
         if (!params.skip_sqanti_qc) {
             if (params.sqanti_qc_cage) {
                 ch_sqanti_qc_cage_bed = PREPARE_REFERENCE.out.sqanti_qc_cage_bed
@@ -242,9 +241,6 @@ workflow DIRECTRNA{
 */
 
 
-    // Combine genome fasta with genome fasta index into single channel
-    ch_genome_fasta_with_index = ch_genome_fasta.combine(ch_genome_fasta_index)
-
     // Mapping and sorting
     // SUBWORKFLOW: MAPPING
     //
@@ -347,6 +343,7 @@ workflow DIRECTRNA{
         ch_versions = ch_versions.mix(GFFREAD_GETFASTA.out.versions.first())
         }
 
+    // TODO
     // ISOQUANT
    // if (!params.skip_isoquant) {
    //     ISOQUANT( ch_mixed_bam, ch_annotation_gtf, ch_genome_fasta)
@@ -424,13 +421,12 @@ workflow DIRECTRNA{
         }
 
     //
-    // Transcript quantification
+    // Transcript quantification will be added in first update to pipeline
     // TransSigner
     //if (!params.skip_quantification && !params.skip_mapping)
     //    TRANSIGNER_MAP
     //    TRANSIGNER_
     //    TRANSIGNER_QUANT
-
 */
 
     //