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sanger-tol · Jul 18, 2023 · 99816ae · 99816ae
1 parent d9cf87f
commit 99816ae
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Showing 5 changed files with 23 additions and 22 deletions.
diff --git a/README.md b/README.md
@@ -57,15 +57,25 @@ Now, you can run the pipeline using:
 <!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
 
 ```bash
+// For ALL_FILES run
 nextflow run sanger-tol/curationpretext \
    -profile <docker/singularity/.../institute> \
    --fasta path/to/assembly.fa \
    --cram path/to/cram/ \
    --pacbio path/to/pacbio/fasta/ \
    --teloseq TTAGGG \
-   -entry { ALL_FILES | MAPS_ONLY } \
+   --sample { default is "pretext_rerun" }
+   -entry ALL_FILES \
    --outdir path/to/outdir/
 
+// For MAPS_ONLY run
+nextflow run sanger-tol/curationpretext \
+   -profile <docker/singularity/.../institute> \
+   --fasta path/to/assembly.fa \
+   --cram path/to/cram/ \
+   --sample { default is "pretext_rerun" }
+   -entry MAPS_ONLY \
+   --outdir path/to/outdir/
 ```
 
 > **Warning:**

diff --git a/conf/base.config b/conf/base.config
@@ -16,7 +16,7 @@ process {
     time   = { check_max( 4.h  * task.attempt, 'time'   ) }
 
     errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
-    maxRetries    = 1
+    maxRetries    = 2
     maxErrors     = '-1'
 
     withName: '.*:.*:LONGREAD_COVERAGE:(MINIMAP2_ALIGN|MINIMAP2_ALIGN_SPLIT)' {
@@ -26,7 +26,7 @@ process {
 
     withName: CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT {
         cpus    = { check_max( 16      * 1, 'cpus'   ) }
-        memory  = { check_max( 50.GB  * task.attempt, 'memory' ) }
+        memory  = { check_max( 80.GB  * task.attempt, 'memory' ) }
     }
 
     withName: PRETEXTMAP_STANDRD{
@@ -45,7 +45,7 @@ process {
     }
 
     withName: BWAMEM2_INDEX {
-        memory  = { check_max( 40.GB  * task.attempt, 'memory' ) }
+        memory  = { check_max( 100.GB  * task.attempt, 'memory' ) }
     }
 
     // Process-specific resource requirements

diff --git a/lib/WorkflowCurationpretext.groovy b/lib/WorkflowCurationpretext.groovy
@@ -14,8 +14,8 @@ class WorkflowCurationpretext {
         genomeExistsError(params, log)
 
 
-        if (!params.fasta) {
-            Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
+        if (!params.input) {
+            Nextflow.error "Genome fasta file not specified with e.g. '--input genome.fa' or via a detectable config file."
         }
     }
 

diff --git a/nextflow.config b/nextflow.config
@@ -11,7 +11,7 @@ params {
 
     // Input options
     input                      = null
-    sample                     = "david"
+    sample                     = "pretext_rerun"
     teloseq                    = "TTAGGG"
     pacbio                     = null
     cram                       = null
@@ -162,15 +162,6 @@ profiles {
     test_full { includeConfig 'conf/test_full.config' }
 }
 
-
-// Load igenomes.config if required
-if (!params.igenomes_ignore) {
-    includeConfig 'conf/igenomes.config'
-} else {
-    params.genomes = [:]
-}
-
-
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
 // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.

diff --git a/subworkflows/local/generate_maps.nf b/subworkflows/local/generate_maps.nf
@@ -28,7 +28,7 @@ workflow GENERATE_MAPS {
     //
     // MODULE: GENERATE INDEX OF REFERENCE FASTA
     //
-    SAMTOOLS_FAIDX ( 
+    SAMTOOLS_FAIDX (
         reference_tuple,
         [[],[]]
     )
@@ -43,7 +43,7 @@ workflow GENERATE_MAPS {
     )
     ch_versions         = ch_versions.mix(BWAMEM2_INDEX.out.versions)
 
-    Channel.of([[id: 'david'], hic_reads_path]).set { ch_hic_path }
+    Channel.of([[id: 'hic_path'], hic_reads_path]).set { ch_hic_path }
 
     //
     // MODULE: generate a cram csv file containing the required parametres for CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT
@@ -61,9 +61,9 @@ workflow GENERATE_MAPS {
         .combine (reference_tuple)
         .combine (BWAMEM2_INDEX.out.index)
         .map{ cram_id, cram_info, ref_id, ref_dir, bwa_id, bwa_path ->
-            tuple(  [ 
+            tuple(  [
                     id: cram_id.id
-                    ], 
+                    ],
                     file(cram_info[0]),
                     cram_info[1],
                     cram_info[2],
@@ -72,15 +72,15 @@ workflow GENERATE_MAPS {
                     cram_info[5],
                     cram_info[6],
                     bwa_path.toString() + '/' + ref_dir.toString().split('/')[-1]
-            )                          
+            )
         }
        .set { ch_filtering_input }
 
     //
     // MODULE: parallel proccessing bwa-mem2 alignment by given interval of containers from cram files
     //
     CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT (
-        ch_filtering_input 
+        ch_filtering_input
     )
     ch_versions         = ch_versions.mix(CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT.out.versions)