From aba8443bf02b80912e56b44d7d968c5c49913de4 Mon Sep 17 00:00:00 2001
From: Jaron Arbet <[jarbet@mednet.ucla.edu]>
Date: Wed, 31 Aug 2022 11:23:26 -0700
Subject: [PATCH 01/15] attempt switching to common validate module

---
 CHANGELOG.md                 |  1 +
 config/default.config        |  1 -
 main.nf                      |  1 -
 module/align_DNA_BWA_MEM2.nf |  2 +-
 module/align_DNA_HISAT2.nf   |  2 +-
 module/validation.nf         | 23 -----------------------
 6 files changed, 3 insertions(+), 27 deletions(-)
 delete mode 100644 module/validation.nf

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9c26606b..c3310eb5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ## [Unreleased]
 
 ### Changed
+- Replace `blcdsdockerregistry/validate:2.1.5` (out of date) with the version from [pipeline-Nextflow-module](https://github.com/uclahs-cds/pipeline-Nextflow-module/tree/main/modules/PipeVal/validate).
 - Update input csv according to [here](https://confluence.mednet.ucla.edu/pages/viewpage.action?spaceKey=BOUTROSLAB&title=2022-07-27+Nextflow+Working+Group+Meeting+Notes) (Section "Input structures for alignment pipelines")
 - `run_MarkDuplicatesSpark_GATK` now retries once with 130GB on F72, and 140GB on M64
 - Update registered output function
diff --git a/config/default.config b/config/default.config
index aa830e5b..60caf96d 100644
--- a/config/default.config
+++ b/config/default.config
@@ -19,7 +19,6 @@ params {
     docker_image_hisat2_and_samtools = "blcdsdockerregistry/hisat2_samtools-1.12:2.2.1"
     docker_image_picardtools = "blcdsdockerregistry/picard:2.26.10"
     docker_image_sha512sum = "blcdsdockerregistry/align-dna:sha512sum-1.0"
-    docker_image_validate_params = "blcdsdockerregistry/validate:2.1.5"    
     docker_image_gatk = "broadinstitute/gatk:4.2.4.1"
     docker_image_samtools = "blcdsdockerregistry/samtools:1.15.1"
 
diff --git a/main.nf b/main.nf
index b1d1b89d..863da4c0 100644
--- a/main.nf
+++ b/main.nf
@@ -39,7 +39,6 @@ log.info """\
    - HISAT2:  ${params.aligner.contains("HISAT2") ? params.docker_image_hisat2_and_samtools : "None"}
    - Picard Tools: ${params.docker_image_picardtools}
    - sha512sum: ${params.docker_image_sha512sum}
-   - validate_params: ${params.docker_image_validate_params}
    - GATK: ${params.docker_image_gatk}
 
    ------------------------------------
diff --git a/module/align_DNA_BWA_MEM2.nf b/module/align_DNA_BWA_MEM2.nf
index 671bea8f..b8f0fd15 100644
--- a/module/align_DNA_BWA_MEM2.nf
+++ b/module/align_DNA_BWA_MEM2.nf
@@ -3,7 +3,7 @@
 // here it actually saves cost, time, and memory to directly pipe the output into 
 // samtools due to the large size of the uncompressed SAM files.
 include { run_sort_SAMtools ; run_merge_SAMtools } from './samtools.nf'
-include { run_validate_PipeVal; run_validate_PipeVal as validate_output_file } from './validation.nf'
+include { run_validate_PipeVal; run_validate_PipeVal as validate_output_file } from '..external/nextflow-modules/modules/PipeVal/validate/main.nf'
 include { run_MarkDuplicate_Picard } from './mark_duplicate_picardtools.nf'
 include { run_MarkDuplicatesSpark_GATK } from './mark_duplicates_spark.nf'
 include { generate_sha512sum } from './check_512sum.nf'
diff --git a/module/align_DNA_HISAT2.nf b/module/align_DNA_HISAT2.nf
index f2ad499d..858ed311 100644
--- a/module/align_DNA_HISAT2.nf
+++ b/module/align_DNA_HISAT2.nf
@@ -4,7 +4,7 @@
 // samtools due to the large size of the uncompressed SAM files.
 
 include { run_sort_SAMtools ; run_merge_SAMtools} from './samtools.nf'
-include { run_validate_PipeVal; run_validate_PipeVal as validate_output_file } from './validation.nf'
+include { run_validate_PipeVal; run_validate_PipeVal as validate_output_file } from '..external/nextflow-modules/modules/PipeVal/validate/main.nf'
 include { run_MarkDuplicate_Picard } from './mark_duplicate_picardtools.nf'
 include { run_MarkDuplicatesSpark_GATK } from './mark_duplicates_spark.nf'
 include { generate_sha512sum } from './check_512sum.nf'
diff --git a/module/validation.nf b/module/validation.nf
deleted file mode 100644
index ab641392..00000000
--- a/module/validation.nf
+++ /dev/null
@@ -1,23 +0,0 @@
-process run_validate_PipeVal {
-   container params.docker_image_validate_params
-
-   publishDir path: "${log_output_dir}/${task.process.split(':')[-1].replace('_', '-')}/${task.index}",
-      pattern: ".command.*",
-      mode: "copy",
-      saveAs: { "log${file(it).getName()}" }
-
-   input:
-   path(file_to_validate)
-   val(log_output_dir)
-
-   output:
-   path(".command.*")
-   path("input_validation.txt"), emit: val_file
-
-   script:
-   """
-   set -euo pipefail
-
-   python -m validate -t file-input ${file_to_validate} > "input_validation.txt"
-   """
-   }

From d6771826b8f5f98f0c429beda0e0f533cd6504f1 Mon Sep 17 00:00:00 2001
From: Jaron Arbet <[jarbet@mednet.ucla.edu]>
Date: Wed, 31 Aug 2022 11:34:36 -0700
Subject: [PATCH 02/15] external filepath

---
 module/align_DNA_BWA_MEM2.nf | 2 +-
 module/align_DNA_HISAT2.nf   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/module/align_DNA_BWA_MEM2.nf b/module/align_DNA_BWA_MEM2.nf
index b8f0fd15..a5bed807 100644
--- a/module/align_DNA_BWA_MEM2.nf
+++ b/module/align_DNA_BWA_MEM2.nf
@@ -3,7 +3,7 @@
 // here it actually saves cost, time, and memory to directly pipe the output into 
 // samtools due to the large size of the uncompressed SAM files.
 include { run_sort_SAMtools ; run_merge_SAMtools } from './samtools.nf'
-include { run_validate_PipeVal; run_validate_PipeVal as validate_output_file } from '..external/nextflow-modules/modules/PipeVal/validate/main.nf'
+include { run_validate_PipeVal; run_validate_PipeVal as validate_output_file } from '../external/nextflow-modules/modules/PipeVal/validate/main.nf'
 include { run_MarkDuplicate_Picard } from './mark_duplicate_picardtools.nf'
 include { run_MarkDuplicatesSpark_GATK } from './mark_duplicates_spark.nf'
 include { generate_sha512sum } from './check_512sum.nf'
diff --git a/module/align_DNA_HISAT2.nf b/module/align_DNA_HISAT2.nf
index 858ed311..90f88c88 100644
--- a/module/align_DNA_HISAT2.nf
+++ b/module/align_DNA_HISAT2.nf
@@ -4,7 +4,7 @@
 // samtools due to the large size of the uncompressed SAM files.
 
 include { run_sort_SAMtools ; run_merge_SAMtools} from './samtools.nf'
-include { run_validate_PipeVal; run_validate_PipeVal as validate_output_file } from '..external/nextflow-modules/modules/PipeVal/validate/main.nf'
+include { run_validate_PipeVal; run_validate_PipeVal as validate_output_file } from '../external/nextflow-modules/modules/PipeVal/validate/main.nf'
 include { run_MarkDuplicate_Picard } from './mark_duplicate_picardtools.nf'
 include { run_MarkDuplicatesSpark_GATK } from './mark_duplicates_spark.nf'
 include { generate_sha512sum } from './check_512sum.nf'

From d5bcc29dc5d076f837cdd0c5793c44d146f53218 Mon Sep 17 00:00:00 2001
From: Jaron Arbet <[jarbet@mednet.ucla.edu]>
Date: Wed, 31 Aug 2022 13:58:17 -0700
Subject: [PATCH 03/15] dont remove docker_image_validate_params

---
 config/default.config | 1 +
 main.nf               | 1 +
 2 files changed, 2 insertions(+)

diff --git a/config/default.config b/config/default.config
index 60caf96d..c4f5437b 100644
--- a/config/default.config
+++ b/config/default.config
@@ -19,6 +19,7 @@ params {
     docker_image_hisat2_and_samtools = "blcdsdockerregistry/hisat2_samtools-1.12:2.2.1"
     docker_image_picardtools = "blcdsdockerregistry/picard:2.26.10"
     docker_image_sha512sum = "blcdsdockerregistry/align-dna:sha512sum-1.0"
+    docker_image_validate_params = "blcdsdockerregistry/validate:2.1.5"
     docker_image_gatk = "broadinstitute/gatk:4.2.4.1"
     docker_image_samtools = "blcdsdockerregistry/samtools:1.15.1"
 
diff --git a/main.nf b/main.nf
index 863da4c0..b1d1b89d 100644
--- a/main.nf
+++ b/main.nf
@@ -39,6 +39,7 @@ log.info """\
    - HISAT2:  ${params.aligner.contains("HISAT2") ? params.docker_image_hisat2_and_samtools : "None"}
    - Picard Tools: ${params.docker_image_picardtools}
    - sha512sum: ${params.docker_image_sha512sum}
+   - validate_params: ${params.docker_image_validate_params}
    - GATK: ${params.docker_image_gatk}
 
    ------------------------------------

From ea041dfe27249fe0d8c209f9140b0a0c382cd012 Mon Sep 17 00:00:00 2001
From: Jaron Arbet <[jarbet@mednet.ucla.edu]>
Date: Wed, 31 Aug 2022 13:59:09 -0700
Subject: [PATCH 04/15] validate v2.1.6

---
 config/default.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/default.config b/config/default.config
index c4f5437b..ea4d7954 100644
--- a/config/default.config
+++ b/config/default.config
@@ -19,7 +19,7 @@ params {
     docker_image_hisat2_and_samtools = "blcdsdockerregistry/hisat2_samtools-1.12:2.2.1"
     docker_image_picardtools = "blcdsdockerregistry/picard:2.26.10"
     docker_image_sha512sum = "blcdsdockerregistry/align-dna:sha512sum-1.0"
-    docker_image_validate_params = "blcdsdockerregistry/validate:2.1.5"
+    docker_image_validate_params = "blcdsdockerregistry/validate:2.1.6"
     docker_image_gatk = "broadinstitute/gatk:4.2.4.1"
     docker_image_samtools = "blcdsdockerregistry/samtools:1.15.1"
 

From 75529bba9da5717d0e6eb1ba1414aecaab2d4b01 Mon Sep 17 00:00:00 2001
From: Jaron Arbet <[jarbet@mednet.ucla.edu]>
Date: Wed, 31 Aug 2022 14:09:20 -0700
Subject: [PATCH 05/15] validate_output_file should only take 1 input

---
 module/align_DNA_BWA_MEM2.nf | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/module/align_DNA_BWA_MEM2.nf b/module/align_DNA_BWA_MEM2.nf
index a5bed807..b4538cc1 100644
--- a/module/align_DNA_BWA_MEM2.nf
+++ b/module/align_DNA_BWA_MEM2.nf
@@ -3,7 +3,13 @@
 // here it actually saves cost, time, and memory to directly pipe the output into 
 // samtools due to the large size of the uncompressed SAM files.
 include { run_sort_SAMtools ; run_merge_SAMtools } from './samtools.nf'
-include { run_validate_PipeVal; run_validate_PipeVal as validate_output_file } from '../external/nextflow-modules/modules/PipeVal/validate/main.nf'
+include { run_validate_PipeVal; run_validate_PipeVal as validate_output_file } from '../external/nextflow-modules/modules/PipeVal/validate/main.nf' addParams(
+    options: [
+        docker_image_version: params.pipeval_version,
+        process_label: 'process_low',
+        main_process: "BWA-MEM2-${params.bwa_version}"
+        ]
+    )
 include { run_MarkDuplicate_Picard } from './mark_duplicate_picardtools.nf'
 include { run_MarkDuplicatesSpark_GATK } from './mark_duplicates_spark.nf'
 include { generate_sha512sum } from './check_512sum.nf'
@@ -128,8 +134,7 @@ workflow align_DNA_BWA_MEM2_workflow {
          och_bam.mix(
             och_bam_index,
             Channel.from(params.work_dir, params.output_dir)
-            ),
-            aligner_log_dir
+            )
          )
       validate_output_file.out.val_file.collectFile(
          name: 'output_validation.txt',

From e4677fd3014a540934e7ea70137058a9e187c553 Mon Sep 17 00:00:00 2001
From: Jaron Arbet <[jarbet@mednet.ucla.edu]>
Date: Wed, 31 Aug 2022 14:27:45 -0700
Subject: [PATCH 06/15] dont rename run_validate_PipeVal

---
 config/default.config        | 1 +
 module/align_DNA_BWA_MEM2.nf | 9 ++++-----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/config/default.config b/config/default.config
index ea4d7954..605525a8 100644
--- a/config/default.config
+++ b/config/default.config
@@ -14,6 +14,7 @@ params {
     // tools and their versions
     bwa_version = "BWA-MEM2-2.2.1"
     hisat2_version = "HISAT2-2.2.1"
+    pipeval_version = "2.1.6"
 
     docker_image_bwa_and_samtools = "blcdsdockerregistry/bwa-mem2_samtools-1.12:2.2.1"
     docker_image_hisat2_and_samtools = "blcdsdockerregistry/hisat2_samtools-1.12:2.2.1"
diff --git a/module/align_DNA_BWA_MEM2.nf b/module/align_DNA_BWA_MEM2.nf
index b4538cc1..783b193f 100644
--- a/module/align_DNA_BWA_MEM2.nf
+++ b/module/align_DNA_BWA_MEM2.nf
@@ -3,7 +3,7 @@
 // here it actually saves cost, time, and memory to directly pipe the output into 
 // samtools due to the large size of the uncompressed SAM files.
 include { run_sort_SAMtools ; run_merge_SAMtools } from './samtools.nf'
-include { run_validate_PipeVal; run_validate_PipeVal as validate_output_file } from '../external/nextflow-modules/modules/PipeVal/validate/main.nf' addParams(
+include { run_validate_PipeVal } from '../external/nextflow-modules/modules/PipeVal/validate/main.nf' addParams(
     options: [
         docker_image_version: params.pipeval_version,
         process_label: 'process_low',
@@ -89,8 +89,7 @@ workflow align_DNA_BWA_MEM2_workflow {
       run_validate_PipeVal(ich_samples_validate.mix(
          ich_reference_fasta,
          ich_reference_index_files
-         ),
-         aligner_log_dir
+         )
          )
 
       // change validation file name depending on whether inputs or outputs are being validated
@@ -130,13 +129,13 @@ workflow align_DNA_BWA_MEM2_workflow {
          }
       }
       generate_sha512sum(och_bam_index.mix(och_bam), aligner_output_dir)
-      validate_output_file(
+      run_validate_PipeVal(
          och_bam.mix(
             och_bam_index,
             Channel.from(params.work_dir, params.output_dir)
             )
          )
-      validate_output_file.out.val_file.collectFile(
+      run_validate_PipeVal.out.val_file.collectFile(
          name: 'output_validation.txt',
          storeDir: "${aligner_validation_dir}"
          )

From 73f9547232da128369aa4dc46384ec6b24226311 Mon Sep 17 00:00:00 2001
From: Jaron Arbet <[jarbet@mednet.ucla.edu]>
Date: Wed, 31 Aug 2022 14:41:53 -0700
Subject: [PATCH 07/15] run_validate_PipeVal.out.validation_result

---
 module/align_DNA_BWA_MEM2.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/module/align_DNA_BWA_MEM2.nf b/module/align_DNA_BWA_MEM2.nf
index 783b193f..9732e74d 100644
--- a/module/align_DNA_BWA_MEM2.nf
+++ b/module/align_DNA_BWA_MEM2.nf
@@ -94,7 +94,7 @@ workflow align_DNA_BWA_MEM2_workflow {
 
       // change validation file name depending on whether inputs or outputs are being validated
       //val_filename = ${task.process.split(':')[1].replace('_', '-')} == run-validate ? "input_validation.txt" : "output_validation.txt"
-      run_validate_PipeVal.out.val_file.collectFile(
+      run_validate_PipeVal.out.validation_result.collectFile(
          name: 'input_validation.txt',
          storeDir: "${aligner_validation_dir}"
          )
@@ -135,7 +135,7 @@ workflow align_DNA_BWA_MEM2_workflow {
             Channel.from(params.work_dir, params.output_dir)
             )
          )
-      run_validate_PipeVal.out.val_file.collectFile(
+      run_validate_PipeVal.out.validation_result.collectFile(
          name: 'output_validation.txt',
          storeDir: "${aligner_validation_dir}"
          )

From 26a09f4da6e37dc2d5382db96ded18f3e71c2e82 Mon Sep 17 00:00:00 2001
From: Jaron Arbet <[jarbet@mednet.ucla.edu]>
Date: Wed, 31 Aug 2022 15:15:04 -0700
Subject: [PATCH 08/15] pipeval v 3.0.0

---
 config/default.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/default.config b/config/default.config
index 605525a8..9c9ffa19 100644
--- a/config/default.config
+++ b/config/default.config
@@ -14,7 +14,7 @@ params {
     // tools and their versions
     bwa_version = "BWA-MEM2-2.2.1"
     hisat2_version = "HISAT2-2.2.1"
-    pipeval_version = "2.1.6"
+    pipeval_version = "3.0.0"
 
     docker_image_bwa_and_samtools = "blcdsdockerregistry/bwa-mem2_samtools-1.12:2.2.1"
     docker_image_hisat2_and_samtools = "blcdsdockerregistry/hisat2_samtools-1.12:2.2.1"

From 41b03800bef85d2ae9359e0a6e56914b6353721c Mon Sep 17 00:00:00 2001
From: Jaron Arbet <[jarbet@mednet.ucla.edu]>
Date: Wed, 31 Aug 2022 15:28:36 -0700
Subject: [PATCH 09/15] cant call run-validate_PipeVal twice, need to rename

---
 module/align_DNA_BWA_MEM2.nf | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/module/align_DNA_BWA_MEM2.nf b/module/align_DNA_BWA_MEM2.nf
index 9732e74d..37f568aa 100644
--- a/module/align_DNA_BWA_MEM2.nf
+++ b/module/align_DNA_BWA_MEM2.nf
@@ -10,6 +10,14 @@ include { run_validate_PipeVal } from '../external/nextflow-modules/modules/Pipe
         main_process: "BWA-MEM2-${params.bwa_version}"
         ]
     )
+// calling run_validate_PipeVal twice causes an error.  The error message says to either rename it (which I'm trying now) or to 'reuse within a different workflow context' (?)
+include { run_validate_PipeVal; run_validate_PipeVal as validate_output_file } from '../external/nextflow-modules/modules/PipeVal/validate/main.nf' addParams(
+    options: [
+        docker_image_version: params.pipeval_version,
+        process_label: 'process_low',
+        main_process: "BWA-MEM2-${params.bwa_version}"
+        ]
+    )
 include { run_MarkDuplicate_Picard } from './mark_duplicate_picardtools.nf'
 include { run_MarkDuplicatesSpark_GATK } from './mark_duplicates_spark.nf'
 include { generate_sha512sum } from './check_512sum.nf'
@@ -129,13 +137,13 @@ workflow align_DNA_BWA_MEM2_workflow {
          }
       }
       generate_sha512sum(och_bam_index.mix(och_bam), aligner_output_dir)
-      run_validate_PipeVal(
+      validate_output_file(
          och_bam.mix(
             och_bam_index,
             Channel.from(params.work_dir, params.output_dir)
             )
          )
-      run_validate_PipeVal.out.validation_result.collectFile(
+      validate_output_file.out.validation_result.collectFile(
          name: 'output_validation.txt',
          storeDir: "${aligner_validation_dir}"
          )

From 6e155a84f7d4ee1b76c76f13d7ca5c04f4df1565 Mon Sep 17 00:00:00 2001
From: Jaron Arbet <[jarbet@mednet.ucla.edu]>
Date: Wed, 31 Aug 2022 15:35:56 -0700
Subject: [PATCH 10/15] cant call run_validate_PipeVal twice, need to rename

---
 module/align_DNA_BWA_MEM2.nf | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/module/align_DNA_BWA_MEM2.nf b/module/align_DNA_BWA_MEM2.nf
index 37f568aa..41c4391d 100644
--- a/module/align_DNA_BWA_MEM2.nf
+++ b/module/align_DNA_BWA_MEM2.nf
@@ -3,13 +3,7 @@
 // here it actually saves cost, time, and memory to directly pipe the output into 
 // samtools due to the large size of the uncompressed SAM files.
 include { run_sort_SAMtools ; run_merge_SAMtools } from './samtools.nf'
-include { run_validate_PipeVal } from '../external/nextflow-modules/modules/PipeVal/validate/main.nf' addParams(
-    options: [
-        docker_image_version: params.pipeval_version,
-        process_label: 'process_low',
-        main_process: "BWA-MEM2-${params.bwa_version}"
-        ]
-    )
+
 // calling run_validate_PipeVal twice causes an error.  The error message says to either rename it (which I'm trying now) or to 'reuse within a different workflow context' (?)
 include { run_validate_PipeVal; run_validate_PipeVal as validate_output_file } from '../external/nextflow-modules/modules/PipeVal/validate/main.nf' addParams(
     options: [

From 6ffaa5068ff2a73d8860395cd286e8ca091db383 Mon Sep 17 00:00:00 2001
From: Jaron Arbet <[jarbet@mednet.ucla.edu]>
Date: Fri, 2 Sep 2022 14:24:25 -0700
Subject: [PATCH 11/15] docker validate params v 3.0.0

---
 config/default.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/default.config b/config/default.config
index 9c9ffa19..e1dc9c36 100644
--- a/config/default.config
+++ b/config/default.config
@@ -20,7 +20,7 @@ params {
     docker_image_hisat2_and_samtools = "blcdsdockerregistry/hisat2_samtools-1.12:2.2.1"
     docker_image_picardtools = "blcdsdockerregistry/picard:2.26.10"
     docker_image_sha512sum = "blcdsdockerregistry/align-dna:sha512sum-1.0"
-    docker_image_validate_params = "blcdsdockerregistry/validate:2.1.6"
+    docker_image_validate_params = "blcdsdockerregistry/validate:3.0.0"
     docker_image_gatk = "broadinstitute/gatk:4.2.4.1"
     docker_image_samtools = "blcdsdockerregistry/samtools:1.15.1"
 

From 920b132680ebbed584f5ad629a9cb921b6b6e8a6 Mon Sep 17 00:00:00 2001
From: Jaron Arbet <[jarbet@mednet.ucla.edu]>
Date: Fri, 2 Sep 2022 14:26:06 -0700
Subject: [PATCH 12/15] docker_image_validate_params: replace validate with
 pipeval

---
 config/default.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/default.config b/config/default.config
index e1dc9c36..a63dfa15 100644
--- a/config/default.config
+++ b/config/default.config
@@ -20,7 +20,7 @@ params {
     docker_image_hisat2_and_samtools = "blcdsdockerregistry/hisat2_samtools-1.12:2.2.1"
     docker_image_picardtools = "blcdsdockerregistry/picard:2.26.10"
     docker_image_sha512sum = "blcdsdockerregistry/align-dna:sha512sum-1.0"
-    docker_image_validate_params = "blcdsdockerregistry/validate:3.0.0"
+    docker_image_validate_params = "blcdsdockerregistry/pipeval:3.0.0"
     docker_image_gatk = "broadinstitute/gatk:4.2.4.1"
     docker_image_samtools = "blcdsdockerregistry/samtools:1.15.1"
 

From b0ae698668da69eb2ca8fc67dddb5ef279b98084 Mon Sep 17 00:00:00 2001
From: Jaron Arbet <[jarbet@mednet.ucla.edu]>
Date: Wed, 7 Sep 2022 14:33:05 -0700
Subject: [PATCH 13/15] format

---
 module/align_DNA_BWA_MEM2.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/module/align_DNA_BWA_MEM2.nf b/module/align_DNA_BWA_MEM2.nf
index 41c4391d..419fd02c 100644
--- a/module/align_DNA_BWA_MEM2.nf
+++ b/module/align_DNA_BWA_MEM2.nf
@@ -88,7 +88,8 @@ workflow align_DNA_BWA_MEM2_workflow {
       ich_reference_fasta
       ich_reference_index_files
    main:
-      run_validate_PipeVal(ich_samples_validate.mix(
+      run_validate_PipeVal(
+         ich_samples_validate.mix( //
          ich_reference_fasta,
          ich_reference_index_files
          )

From 34cf06a21d54ede7433205007a44237ee54e0721 Mon Sep 17 00:00:00 2001
From: Jaron Arbet <[jarbet@mednet.ucla.edu]>
Date: Tue, 20 Sep 2022 14:54:56 -0700
Subject: [PATCH 14/15] setup run_validate_PipeVal input to be tuple
 cardinality 2

---
 module/align_DNA_BWA_MEM2.nf | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/module/align_DNA_BWA_MEM2.nf b/module/align_DNA_BWA_MEM2.nf
index 419fd02c..e3a0b242 100644
--- a/module/align_DNA_BWA_MEM2.nf
+++ b/module/align_DNA_BWA_MEM2.nf
@@ -4,7 +4,7 @@
 // samtools due to the large size of the uncompressed SAM files.
 include { run_sort_SAMtools ; run_merge_SAMtools } from './samtools.nf'
 
-// calling run_validate_PipeVal twice causes an error.  The error message says to either rename it (which I'm trying now) or to 'reuse within a different workflow context' (?)
+// need to rename run_validate_PipeVal since using twice.  Use run_validate_PipeVal for input validation; validate_output_file for output validation
 include { run_validate_PipeVal; run_validate_PipeVal as validate_output_file } from '../external/nextflow-modules/modules/PipeVal/validate/main.nf' addParams(
     options: [
         docker_image_version: params.pipeval_version,
@@ -88,13 +88,17 @@ workflow align_DNA_BWA_MEM2_workflow {
       ich_reference_fasta
       ich_reference_index_files
    main:
-      run_validate_PipeVal(
-         ich_samples_validate.mix( //
+
+      run_validate_PipeVal_inputs = ich_samples_validate.mix( //
          ich_reference_fasta,
          ich_reference_index_files
          )
-         )
+         .map { it -> ["file-input", it] }
 
+      run_validate_PipeVal(
+         run_validate_PipeVal_inputs
+         )
+         
       // change validation file name depending on whether inputs or outputs are being validated
       //val_filename = ${task.process.split(':')[1].replace('_', '-')} == run-validate ? "input_validation.txt" : "output_validation.txt"
       run_validate_PipeVal.out.validation_result.collectFile(

From 27f641a54e447e90dda375b0223f63289c9a655e Mon Sep 17 00:00:00 2001
From: Jaron Arbet <[jarbet@mednet.ucla.edu]>
Date: Tue, 20 Sep 2022 15:06:17 -0700
Subject: [PATCH 15/15] setup validate_output_file process inputs to be tuple
 cardinality 2

---
 module/align_DNA_BWA_MEM2.nf | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/module/align_DNA_BWA_MEM2.nf b/module/align_DNA_BWA_MEM2.nf
index e3a0b242..a51805ee 100644
--- a/module/align_DNA_BWA_MEM2.nf
+++ b/module/align_DNA_BWA_MEM2.nf
@@ -136,11 +136,14 @@ workflow align_DNA_BWA_MEM2_workflow {
          }
       }
       generate_sha512sum(och_bam_index.mix(och_bam), aligner_output_dir)
+
+      validate_output_file_inputs = och_bam.mix(
+         och_bam_index,
+         Channel.from(params.work_dir, params.output_dir)
+         )
+         .map { it -> ["file-input", it] }
       validate_output_file(
-         och_bam.mix(
-            och_bam_index,
-            Channel.from(params.work_dir, params.output_dir)
-            )
+         validate_output_file_inputs
          )
       validate_output_file.out.validation_result.collectFile(
          name: 'output_validation.txt',