bump

Author: ctastad

main.nf

@@ -53,9 +53,9 @@ if (params.help) {
 }
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT MODULES/SUBWORKFLOWS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 include { RESOLVI_PREPROCESS } from './modules/local/resolvi_preprocess'
@@ -85,8 +85,6 @@ if (workflow.profile.contains('awsbatch')) {
 }
 
 // Stage config files
-ch_multiqc_config = file("$baseDir/assets/multiqc_config.yaml", checkIfExists: true)
-ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
 ch_output_docs = file("$baseDir/docs/output.md", checkIfExists: true)
 
 /*
@@ -156,26 +154,10 @@ log.info "-\033[2m--------------------------------------------------\033[0m-"
 // Check the hostnames against configured profiles
 checkHostname()
 
-Channel.from(summary.collect{ [it.key, it.value] })
-    .map { k,v -> "<dt>$k</dt><dd><samp>${v ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>" }
-    .reduce { a, b -> return [a, b].join("\n            ") }
-    .map { x -> """
-    id: 'nf-core-resolvinf-summary'
-    description: " - this information is collected when the pipeline is started."
-    section_name: 'nf-core/resolvinf Workflow Summary'
-    section_href: 'https://github.com/nf-core/resolvinf'
-    plot_type: 'html'
-    data: |
-        <dl class=\"dl-horizontal\">
-            $x
-        </dl>
-    """.stripIndent() }
-    .set { ch_workflow_summary }
-
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     MAIN WORKFLOW
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow RESOLVINF {
@@ -187,7 +169,6 @@ workflow RESOLVINF {
     main:
 
     ch_versions = Channel.empty()
-    ch_multiqc_files = Channel.empty()
 
     // Preprocess spatialdata zarr stores
     RESOLVI_PREPROCESS (
@@ -218,15 +199,10 @@ workflow RESOLVINF {
     )
     ch_versions = ch_versions.mix(RESOLVI_VISUALIZE.out.versions.first())
 
-    // Collect files for MultiQC
-    ch_multiqc_files = ch_multiqc_files.mix(RESOLVI_TRAIN.out.logs.collect{it[1]}.ifEmpty([]))
-    ch_multiqc_files = ch_multiqc_files.mix(RESOLVI_ANALYZE.out.reports.collect{it[1]}.ifEmpty([]))
-
     emit:
     adata_final = RESOLVI_ANALYZE.out.adata_final
     model = RESOLVI_TRAIN.out.model
     plots = RESOLVI_VISUALIZE.out.plots
-    multiqc_files = ch_multiqc_files
     versions = ch_versions
 }
 
@@ -254,33 +230,6 @@ process get_software_versions {
     """
 }
 
-/*
- * MultiQC
- */
-process multiqc {
-    publishDir "${params.outdir}/MultiQC", mode: 'copy'
-
-    input:
-    path (multiqc_config) 
-    path (mqc_custom_config) 
-    path ('software_versions/*') 
-    path workflow_summary 
-    path ('resolvi_logs/*') 
-
-    output:
-    path "*multiqc_report.html", emit: report
-    path "*_data"
-    path "multiqc_plots", optional: true
-
-    script:
-    rtitle = custom_runName ? "--title \"$custom_runName\"" : ''
-    rfilename = custom_runName ? "--filename " + custom_runName.replaceAll('\\W','_').replaceAll('_+','_') + "_multiqc_report" : ''
-    custom_config_file = mqc_custom_config.name != 'OPTIONAL_FILE' ? "--config $mqc_custom_config" : ''
-    """
-    multiqc -f $rtitle $rfilename $custom_config_file .
-    """
-}
-
 /*
  * Output Description HTML
  */
@@ -300,9 +249,9 @@ process output_documentation {
 }
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     RUN MAIN WORKFLOW
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow {
@@ -316,15 +265,6 @@ workflow {
     // Get software versions
     get_software_versions()
 
-    // MultiQC
-    multiqc (
-        ch_multiqc_config,
-        ch_multiqc_custom_config.collect().ifEmpty([]),
-        get_software_versions.out.yaml.collect(),
-        ch_workflow_summary.collectFile(name: "workflow_summary_mqc.yaml"),
-        RESOLVINF.out.multiqc_files.collect().ifEmpty([])
-    )
-
     // Output documentation
     output_documentation(
         ch_output_docs
@@ -364,20 +304,6 @@ workflow.onComplete {
     email_fields['summary']['Nextflow Build'] = workflow.nextflow.build
     email_fields['summary']['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
 
-    // On success try attach the multiqc report
-    def mqc_report = null
-    try {
-        if (workflow.success) {
-            mqc_report = multiqc.out.report.getVal()
-            if (mqc_report.getClass() == ArrayList) {
-                log.warn "[nf-core/resolvinf] Found multiple reports from process 'multiqc', will use only one"
-                mqc_report = mqc_report[0]
-            }
-        }
-    } catch (all) {
-        log.warn "[nf-core/resolvinf] Could not attach MultiQC report to summary email"
-    }
-
     // Check if we are only sending emails on failure
     email_address = params.email
     if (!params.email && params.email_on_fail && !workflow.success) {
@@ -396,7 +322,7 @@ workflow.onComplete {
     def email_html = html_template.toString()
 
     // Render the sendmail template
-    def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, baseDir: "$baseDir", mqcFile: mqc_report, mqcMaxSize: params.max_multiqc_email_size ]
+    def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, baseDir: "$baseDir", mqcFile: null, mqcMaxSize: params.max_multiqc_email_size ]
     def sf = new File("$baseDir/assets/sendmail_template.txt")
     def sendmail_template = engine.createTemplate(sf).make(smail_fields)
     def sendmail_html = sendmail_template.toString()
@@ -487,3 +413,4 @@ def checkHostname() {
         }
     }
 }
+

modules/local/environment.yml

@@ -40,7 +40,7 @@ plt.ioff()
 os.makedirs("plots", exist_ok=True)
 
 # Load data
-adata = sc.read_h5ad("${adata}")
+adata = sc.read_h5ad("${meta.id}_analyzed.h5ad")
 
 # Generate basic plots
 try:
@@ -66,6 +66,15 @@ except Exception as e:
 
 logger.info("Visualization completed!")
 EOF
+
+    cat <<-END_VERSIONS > versions.yml
+"${task.process}":
+    scanpy: \$(python -c "import scanpy; print(scanpy.__version__)")
+    matplotlib: \$(python -c "import matplotlib; print(matplotlib.__version__)")
+    seaborn: \$(python -c "import seaborn; print(seaborn.__version__)")
+    pandas: \$(python -c "import pandas; print(pandas.__version__)")
+    numpy: \$(python -c "import numpy; print(numpy.__version__)")
+END_VERSIONS
     """
 
     stub: