nf-core-rnaseq: Add min_mapped_reads advanced option

laxy_backend/views.py

@@ -2122,6 +2122,15 @@ def post(self, request: Request, version=None):
                 job.params, "params.user_genome.annotation_url", None
             )
 
+            # TODO: nf-core /rnaseq specific - this should go into a pipeline specific validation hook in the
+            #       nf-core-rnaseq app that gets called based on the pipeline being started
+            _min_mapped_reads = job.params.get("params").get(
+                "min_mapped_reads", None
+            )
+            if _min_mapped_reads is not None:
+                job.params['min_mapped_reads'] = int(_min_mapped_reads)
+                job.save()
+
             if (
                 (
                     reference_genome_id

laxy_frontend/src/components/pipelines/nf-core-rnaseq/store/module/index.ts

@@ -5,6 +5,7 @@ const initial_state: any = {
     strandedness: 'auto',
     debug_mode: false,
     has_umi: false,
+    min_mapped_reads: 5,
     save_reference_genome: true,
     save_genome_index: false,
 };

laxy_frontend/src/components/pipelines/nf-core-rnaseq/ui/NfCoreRnaSeqSetup.vue

@@ -47,11 +47,27 @@
                   Use UMIs <em>(UMIs must be in the FASTQ header from bcl2fastq demultiplexing, not in the
                     sequence)</em></md-switch>
 
-                <md-switch v-model="save_reference_genome" id="save-reference-genome-toggle" 
-                           name="save-reference-genome-toggle" class="md-primary">Save reference genome</md-switch>
-
-                <md-switch v-model="save_genome_index" id="save-genome-index-toggle" 
-                           name="save-genome-index-toggle" class="md-primary">Save reference genome index</md-switch>
+                <md-layout>
+                  <md-layout>
+                    <md-input-container>
+                      <label>Exclude samples with less this percentage of mapped reads
+                        (<code>--min_mapped_reads</code>)</label>
+                      <md-input type="number" min="0" max="100" v-model="min_mapped_reads"></md-input>
+                    </md-input-container>
+                  </md-layout>
+                  <md-layout md-flex="5" md-vertical-align="center">
+                    <md-button id="minMappedReadshelpButton" @click="openDialog('minMappedReadsHelpPopup')"
+                      class="push-right md-icon-button md-raised md-dense">
+                      <md-icon style="color: #bdbdbd;">help</md-icon>
+                    </md-button>
+                  </md-layout>
+                </md-layout>
+
+                <md-switch v-model="save_reference_genome" id="save-reference-genome-toggle"
+                  name="save-reference-genome-toggle" class="md-primary">Save reference genome</md-switch>
+
+                <md-switch v-model="save_genome_index" id="save-genome-index-toggle" name="save-genome-index-toggle"
+                  class="md-primary">Save reference genome index</md-switch>
               </md-layout>
 
             </md-layout>
@@ -92,6 +108,27 @@
         nf-core/rnaseq does not support 'auto' strandedness. Please select another strandedness option, or another
         pipeline version.
       </banner-notice>
+      <banner-notice v-if="!isValid_min_mapped_reads" type="error" :show-close-button="false">Invalid value for minimum
+        mapped reads - should be an integer between 0 and 100.
+      </banner-notice>
+
+
+      <md-dialog md-open-from="#minMappedReadshelpButton" md-close-to="#minMappedReadshelpButton"
+        id="minMappedReadsHelpPopup" ref="minMappedReadsHelpPopup">
+        <md-dialog-title>Minimum mapped reads</md-dialog-title>
+
+        <md-dialog-content>
+          The nf-core/rnaseq <code>--min_mapped_reads</code> option.<br />
+          Samples with mapping rates less than this are excluded from the final counts matrix and most QC steps.<br />
+          Setting this to below 5% risks some downstream steps failing, since not all tools handle samples with very
+          low mapping rates gracefully.<br />
+        </md-dialog-content>
+
+        <md-dialog-actions>
+          <md-button class="md-primary" @click="closeDialog('minMappedReadsHelpPopup')">Close</md-button>
+        </md-dialog-actions>
+      </md-dialog>
+
     </md-layout>
 
     <md-snackbar md-position="bottom center" ref="snackbar" :md-duration="snackbar_duration">
@@ -239,6 +276,9 @@ export default class PipelineParams extends Vue {
   @Sync("[email protected]_umi")
   public has_umi: boolean;
 
+  @Sync("[email protected]_mapped_reads")
+  public min_mapped_reads: number;
+
   @Sync("[email protected]_reference_genome")
   public save_reference_genome: boolean;
 
@@ -340,13 +380,22 @@ export default class PipelineParams extends Vue {
     return true;
   }
 
+  get isValid_min_mapped_reads() {
+    if (this.min_mapped_reads >= 0 &&
+      this.min_mapped_reads <= 100) {
+      return true;
+    }
+    return false;
+  }
+
   get isValid_params() {
     let is_valid = false;
     if (
       this.isValid_reference_genome &&
       this.isValid_samples_added &&
       this.isValid_duplicate_samples &&
-      this.isValid_strandedness_option
+      this.isValid_strandedness_option &&
+      this.isValid_min_mapped_reads
     ) {
       is_valid = true;
     }

laxy_pipeline_apps/nf-core-rnaseq/templates/job_scripts/nf-core-rnaseq/3.12.0/scripts/run_job.sh

@@ -381,6 +381,9 @@ function get_settings_from_pipeline_config() {
     if [[ "${_has_umi}" == "true" ]]; then
         export UMI_FLAGS=" --with_umi --skip_umi_extract --umitools_umi_separator : "
     fi
+
+    local -i _min_mapped_reads=$(jq --raw-output '.params."nf-core-rnaseq".min_mapped_reads' "${PIPELINE_CONFIG}" || echo "5")
+    export MIN_MAPPED_READS_ARG=" --min_mapped_reads ${_min_mapped_reads} "
 }
 
 function generate_samplesheet() {
@@ -550,6 +553,7 @@ function run_nextflow() {
        --outdir ${JOB_PATH}/output/results \
        ${GENOME_ARGS} \
        ${UMI_FLAGS} \
+       ${MIN_MAPPED_READS_ARG} \
        --aligner star_salmon \
        --pseudo_aligner salmon \
        --save_reference \
@@ -572,6 +576,7 @@ function run_nextflow() {
             --outdir ${JOB_PATH}/output/results \
             ${GENOME_ARGS} \
             ${UMI_FLAGS} \
+            ${MIN_MAPPED_READS_ARG} \
             --aligner star_salmon \
             --pseudo_aligner salmon \
             --save_reference \

laxy_pipeline_apps/nf-core-rnaseq/templates/job_scripts/nf-core-rnaseq/default/input/scripts/run_job.sh

@@ -376,6 +376,9 @@ function get_settings_from_pipeline_config() {
     if [[ "${_has_umi}" == "true" ]]; then
         export UMI_FLAGS=" --with_umi --skip_umi_extract --umitools_umi_separator : "
     fi
+
+    local -i _min_mapped_reads=$(jq --raw-output '.params."nf-core-rnaseq".min_mapped_reads' "${PIPELINE_CONFIG}" || echo "5")
+    export MIN_MAPPED_READS_ARG=" --min_mapped_reads ${_min_mapped_reads} "
 }
 
 function generate_samplesheet() {
@@ -545,6 +548,7 @@ function run_nextflow() {
        --outdir ${JOB_PATH}/output/results \
        ${GENOME_ARGS} \
        ${UMI_FLAGS} \
+       ${MIN_MAPPED_READS_ARG} \
        --aligner star_salmon \
        --pseudo_aligner salmon \
        --save_reference \
@@ -567,6 +571,7 @@ function run_nextflow() {
             --outdir ${JOB_PATH}/output/results \
             ${GENOME_ARGS} \
             ${UMI_FLAGS} \
+            ${MIN_MAPPED_READS_ARG} \
             --aligner star_salmon \
             --pseudo_aligner salmon \
             --save_reference \