diff --git a/main.nf b/main.nf
index 01e933b..f9f3c58 100644
--- a/main.nf
+++ b/main.nf
@@ -26,11 +26,15 @@ include { pipeline_provenance }            from './modules/provenance.nf'
 include { collect_provenance }             from './modules/provenance.nf'
 
 workflow {
+    ch_workflow_metadata = Channel.value([
+	workflow.sessionId,
+	workflow.runName,
+	workflow.manifest.name,
+	workflow.manifest.version,
+	workflow.start,
+    ])
 
-    ch_pipeline_name = Channel.of(workflow.manifest.name)
-    ch_pipeline_version = Channel.of(workflow.manifest.version)
-
-    ch_pipeline_provenance = pipeline_provenance(ch_pipeline_name.combine(ch_pipeline_version))
+    ch_pipeline_provenance = pipeline_provenance(ch_workflow_metadata)
 
     if (params.samplesheet_input != 'NO_FILE') {
 	ch_illumina_fastq = Channel.fromPath(params.samplesheet_input).splitCsv(header: true).map{ it -> [it['ID'], it['R1'], it['R2']] }.filter{ it -> it[1] != null || it[2] != null }
@@ -109,19 +113,26 @@ workflow {
     // [sample_id, [provenance_file_1.yml, provenance_file_2.yml, provenance_file_3.yml...]]
     // At each step, we add another provenance file to the list using the << operator...
     // ...and then concatenate them all together in the 'collect_provenance' process.
-    ch_provenance = ch_provenance.combine(ch_pipeline_provenance).map{ it -> [it[0], [it[1]]] }
-    ch_provenance = ch_provenance.join(hash_ref.out.provenance).map{ it -> [it[0], it[1] << it[2]] }
-    ch_provenance = ch_provenance.join(hash_fastq_short.out.provenance).map{ it -> [it[0], it[1] << it[2]] }
-    ch_provenance = ch_provenance.join(hash_fastq_long.out.provenance).map{ it -> [it[0], it[1] << it[2]] }
-    ch_provenance = ch_provenance.join(bwa_mem.out.provenance).map{ it -> [it[0], it[1] << it[2]] }
-    ch_provenance = ch_provenance.join(nanoq_pre_filter.out.provenance).map{ it -> [it[0], it[1] << it[2]] }
-    ch_provenance = ch_provenance.join(filtlong.out.provenance).map{ it -> [it[0], it[1] << it[2]] }
-    ch_provenance = ch_provenance.join(nanoq_post_filter.out.provenance).map{ it -> [it[0], it[1] << it[2]] }
-    ch_provenance = ch_provenance.join(minimap2.out.provenance).map{ it -> [it[0], it[1] << it[2]] }
-    ch_provenance = ch_provenance.join(qualimap_bamqc.out.provenance).map{ it -> [it[0], it[1] << it[2]] }
-    ch_provenance = ch_provenance.join(samtools_mpileup.out.provenance).map{ it -> [it[0], it[1] << it[2]] }
-    ch_provenance = ch_provenance.join(samtools_stats.out.provenance).map{ it -> [it[0], it[1] << it[2]] }
-    ch_provenance = ch_provenance.join(freebayes.out.provenance).map{ it -> [it[0], it[1] << it[2]] }
+    ch_provenance = ch_provenance.combine(ch_pipeline_provenance).map{ it ->        [it[0], [it[1]]] }
+    ch_provenance = ch_provenance.join(hash_ref.out.provenance).map{ it ->          [it[0], it[1] << it[2]] }
+    ch_provenance = ch_provenance.join(hash_fastq_short.out.provenance).map{ it ->  [it[0], it[1] << it[2]] }
+    // Check the length of the collected nanopore sample IDs to determine if we need to collect nanopore provenance
+    // I need to pull the value out of the channel and convert it to a list to get the length
+    ch_illumina_sample_ids.toList().size().view()
+    if (false) {
+	ch_provenance = ch_provenance.join(hash_fastq_long.out.provenance).map{ it ->   [it[0], it[1] << it[2]] }
+    }
+    ch_provenance = ch_provenance.join(bwa_mem.out.provenance).map{ it ->           [it[0], it[1] << it[2]] }
+    if (false) {
+	ch_provenance = ch_provenance.join(nanoq_pre_filter.out.provenance).map{ it ->  [it[0], it[1] << it[2]] }
+	ch_provenance = ch_provenance.join(filtlong.out.provenance).map{ it ->          [it[0], it[1] << it[2]] }
+	ch_provenance = ch_provenance.join(nanoq_post_filter.out.provenance).map{ it -> [it[0], it[1] << it[2]] }
+	ch_provenance = ch_provenance.join(minimap2.out.provenance).map{ it ->          [it[0], it[1] << it[2]] }
+    }
+    ch_provenance = ch_provenance.join(qualimap_bamqc.out.provenance).map{ it ->    [it[0], it[1] << it[2]] }
+    ch_provenance = ch_provenance.join(samtools_mpileup.out.provenance).map{ it ->  [it[0], it[1] << it[2]] }
+    ch_provenance = ch_provenance.join(samtools_stats.out.provenance).map{ it ->    [it[0], it[1] << it[2]] }
+    ch_provenance = ch_provenance.join(freebayes.out.provenance).map{ it ->         [it[0], it[1] << it[2]] }
 
     collect_provenance(ch_provenance)
   
diff --git a/modules/alignment_variants.nf b/modules/alignment_variants.nf
index 34b6f01..65639dc 100644
--- a/modules/alignment_variants.nf
+++ b/modules/alignment_variants.nf
@@ -54,14 +54,18 @@ process bwa_mem {
     printf -- "      parameters:\\n"           >> ${sample_id}_bwa_mem_provenance.yml
     printf -- "        - parameter: -m\\n"     >> ${sample_id}_bwa_mem_provenance.yml
     printf -- "          value: null\\n"       >> ${sample_id}_bwa_mem_provenance.yml
+    if [ ! "${params.skip_alignment_cleaning}" == "true" ]; then
     printf -- "        - parameter: -r\\n"     >> ${sample_id}_bwa_mem_provenance.yml
     printf -- "          value: null\\n"       >> ${sample_id}_bwa_mem_provenance.yml
+    fi
     printf -- "    - tool_name: samtools\\n"   >> ${sample_id}_bwa_mem_provenance.yml
     printf -- "      tool_version: \$(samtools 2>&1 | grep 'Version' | cut -d ' ' -f 2)\\n" >> ${sample_id}_bwa_mem_provenance.yml
     printf -- "      subcommand: markdup\\n"      >> ${sample_id}_bwa_mem_provenance.yml
+    if [ ! "${params.skip_alignment_cleaning}" == "true" ]; then
     printf -- "      parameters:\\n"           >> ${sample_id}_bwa_mem_provenance.yml
     printf -- "        - parameter: -r\\n"     >> ${sample_id}_bwa_mem_provenance.yml
     printf -- "          value: null\\n"       >> ${sample_id}_bwa_mem_provenance.yml
+    fi
 
     bwa mem \
 	-t ${bwa_threads} \
@@ -190,7 +194,7 @@ process samtools_stats {
 
     tag { sample_id + ' / ' + short_long }
 
-    publishDir "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_${short_long}_samtools_stats*"
+    publishDir "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_${short_long}_samtools_stats*.{txt,tsv,csv}"
 
     input:
     tuple val(sample_id), val(short_long), path(alignment)
diff --git a/modules/provenance.nf b/modules/provenance.nf
index af4218d..f2a0e2d 100644
--- a/modules/provenance.nf
+++ b/modules/provenance.nf
@@ -5,34 +5,37 @@ process pipeline_provenance {
     executor 'local'
 
     input:
-    tuple val(pipeline_name), val(pipeline_version)
+    tuple val(session_id), val(run_name), val(pipeline_name), val(pipeline_version), val(timestamp_analysis_start)
 
     output:
     file("pipeline_provenance.yml")
 
     script:
     """
-    printf -- "- pipeline_name: ${pipeline_name}\\n"       >> pipeline_provenance.yml
-    printf -- "  pipeline_version: ${pipeline_version}\\n" >> pipeline_provenance.yml
-  """
+    printf -- "- pipeline_name: ${pipeline_name}\\n"                       >> pipeline_provenance.yml
+    printf -- "  pipeline_version: ${pipeline_version}\\n"                 >> pipeline_provenance.yml
+    printf -- "  nextflow_session_id: ${session_id}\\n"                    >> pipeline_provenance.yml
+    printf -- "  nextflow_run_name: ${run_name}\\n"                        >> pipeline_provenance.yml
+    printf -- "  timestamp_analysis_start: ${timestamp_analysis_start}\\n" >> pipeline_provenance.yml
+    """
 }
 
 process collect_provenance {
 
-  tag { sample_id }
-
-  executor 'local'
+    tag { sample_id }
+    
+    executor 'local'
 
-  publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_*_provenance.yml", mode: 'copy'
+    publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_*_provenance.yml", mode: 'copy'
 
-  input:
-  tuple val(sample_id), path(provenance_files)
+    input:
+    tuple val(sample_id), path(provenance_files)
 
-  output:
-  tuple val(sample_id), file("${sample_id}_*_provenance.yml")
+    output:
+    tuple val(sample_id), file("${sample_id}_*_provenance.yml")
 
-  script:
-  """
-  cat ${provenance_files} > ${sample_id}_\$(date +%Y%m%d%H%M%S)_provenance.yml
-  """
+    script:
+    """
+    cat ${provenance_files} > ${sample_id}_\$(date +%Y%m%d%H%M%S)_provenance.yml
+    """
 }