Merge pull request #30 from uclahs-cds/cz-update-output-dir

fixed error: Unknown method invocation `includeConfig`

Author: Chenghao Zhu

README.md

@@ -37,6 +37,18 @@ Pipelines should be run **WITH A SINGLE SAMPLE AT TIME**. Otherwise resource all
 
 4. See the submission script, [here](https://github.com/uclahs-cds/tool-submit-nf), to submit your pipeline
 
+<b><i> BWA-MEM2 Genome Index </i></b>
+The genome index files must be generated by BWA-MEM2 with the correct version. Neither the index from previous version of BWA-MEM2, or from BWA can be accepted. The index files can be generated from a custom genome FASTA using the command below:
+
+```
+docker run \
+    -it --rm \
+    -v $(pwd):$(pwd) \
+    -w $(pwd) \
+    blcdsdockerregistry/align-dna:bwa-mem2-2.1_samtools-1.10 \
+    bwa-mem2 index genome.fa 
+```
+
 ---
 
 ## Flow Diagram

pipeline/align-DNA.nf

@@ -143,7 +143,7 @@ process validate_inputs {
 }
 
 // align with bwa mem and convert with samtools
-process BWA_mem_SAMtools_Convert_Sam_to_Bam {
+process align_BWA_mem_convert_SAM_to_BAM_samtools {
    container dockeri_BWA_and_SAMtools
 
    publishDir path: params.bam_output_dir,
@@ -154,7 +154,7 @@ process BWA_mem_SAMtools_Convert_Sam_to_Bam {
    publishDir path: params.log_output_dir,
       pattern: ".command.*",
       mode: "copy",
-      saveAs: { "BWA_mem_SAMtools_Convert_Sam_to_Bam/${file(read1_fastq).getName()}/log${file(it).getName()}" }
+      saveAs: { "align_BWA_mem_convert_SAM_to_BAM_samtools/${file(read1_fastq).getSimpleName()}/log${file(it).getName()}" }
 
    memory amount_of_memory
    cpus params.bwa_mem_number_of_cpus
@@ -176,7 +176,7 @@ process BWA_mem_SAMtools_Convert_Sam_to_Bam {
       tuple(val(library), 
          val(lane),
          file("${library}-${lane}.aligned.bam")
-      ) into och_BWA_mem_SAMtools_Convert_Sam_to_Bam
+      ) into och_align_BWA_mem_convert_SAM_to_BAM_samtools
       file ".command.*"
 
    script:
@@ -221,7 +221,7 @@ process PicardTools_SortSam  {
       tuple(val(library), 
          val(lane),
          file(input_bam)
-      ) from och_BWA_mem_SAMtools_Convert_Sam_to_Bam
+      ) from och_align_BWA_mem_convert_SAM_to_BAM_samtools
 
    // the first value of the tuple will be used as a key to group aligned and filtered bams
    // from the same sample and library but different lane together

pipeline/config/align-DNA.config

@@ -1,4 +1,4 @@
-includeConfig "${projectDir}/config/_pipeline.config"
+includeConfig "${projectDir}/config/methods.config"
 
 params {
     // sample inputs

pipeline/config/methods.config

@@ -4,7 +4,7 @@ manifest {
     name = "align-DNA"
     author = "Benjamin Carlin"
     description = "alignment pipeline for paired fastqs DNA samples"
-    version = "6.0.0"
+    version = "6.0.1"
 }
 
 params {
@@ -66,7 +66,7 @@ methods {
                     "Please double check the input.csv: ${params.input_csv} "
                 )
             }
-        } else {
+        } else if (params.blcds_registered_dataset_output) {
             // TODO: need to valid dataset information
             if (!params.containsKey("blcds_disease_id") || !params.containsKey("blcds_dataset_id") ||
                 !params.containsKey("blcds_patient_id") || !params.containsKey("blcds_sample_id") ||
@@ -147,12 +147,22 @@ methods {
         process.cache = params.cache_intermediate_pipeline_steps
     }
 
+    set_docker_sudo = {
+        if (params.containsKey("blcds_cluster_slurm") && (!params.blcds_cluster_slurm)) {
+            docker.sudo = true
+        }
+        if (params.containsKey("blcds_mount_dir") && (params.blcds_mount_dir == '/data')) {
+            docker.sudo = true
+        }
+    }
+
     setup = {
         methods.set_output_dir()
         methods.set_env()
         methods.set_process()
         methods.set_timeline()
         methods.set_trace()
         methods.set_report()
+        methods.set_docker_sudo()
     }
 }