From cede72a367150268ecd1f8470b26ef6fb4e65466 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 10 Oct 2023 12:08:44 -0400
Subject: [PATCH 01/10] feat: khmer/uniquekmers module w/ stubs

---
 modules/CCBR/khmer/uniquekmers/main.nf        | 48 +++++++++++++++++++
 modules/CCBR/khmer/uniquekmers/meta.yml       | 42 ++++++++++++++++
 tests/modules/CCBR/khmer/uniquekmers/main.nf  | 12 +++++
 .../CCBR/khmer/uniquekmers/nextflow.config    |  5 ++
 tests/modules/CCBR/khmer/uniquekmers/test.yml | 10 ++++
 5 files changed, 117 insertions(+)
 create mode 100644 modules/CCBR/khmer/uniquekmers/main.nf
 create mode 100644 modules/CCBR/khmer/uniquekmers/meta.yml
 create mode 100644 tests/modules/CCBR/khmer/uniquekmers/main.nf
 create mode 100644 tests/modules/CCBR/khmer/uniquekmers/nextflow.config
 create mode 100644 tests/modules/CCBR/khmer/uniquekmers/test.yml

diff --git a/modules/CCBR/khmer/uniquekmers/main.nf b/modules/CCBR/khmer/uniquekmers/main.nf
new file mode 100644
index 0000000..fca4d5c
--- /dev/null
+++ b/modules/CCBR/khmer/uniquekmers/main.nf
@@ -0,0 +1,48 @@
+process KHMER_UNIQUEKMERS {
+    tag "$fasta"
+    label 'process_low'
+
+    conda "bioconda::khmer=3.0.0a3"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/khmer:3.0.0a3--py37haa7609a_2' :
+        'biocontainers/khmer:3.0.0a3--py37haa7609a_2' }"
+
+    input:
+    path fasta
+    val  kmer_size
+
+    output:
+    path "report.txt"  , emit: report
+    path "kmers.txt"   , emit: kmers
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    unique-kmers.py \\
+        -k $kmer_size \\
+        -R report.txt \\
+        $args \\
+        $fasta
+
+    grep ^number report.txt | sed 's/^.*:.[[:blank:]]//g' > kmers.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        khmer: \$( unique-kmers.py --version 2>&1 | grep ^khmer | sed 's/^khmer //;s/ .*\$//' )
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch report.txt khmers.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        khmer: \$( unique-kmers.py --version 2>&1 | grep ^khmer | sed 's/^khmer //;s/ .*\$//' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/CCBR/khmer/uniquekmers/meta.yml b/modules/CCBR/khmer/uniquekmers/meta.yml
new file mode 100644
index 0000000..5ffb451
--- /dev/null
+++ b/modules/CCBR/khmer/uniquekmers/meta.yml
@@ -0,0 +1,42 @@
+name: "khmer_uniquekmers"
+description: In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more. Adapted from nf-core/modules khmer/uniquekhmers.
+keywords:
+  - khmer
+  - k-mer
+  - effective genome size
+
+tools:
+  - "khmer":
+      description: khmer k-mer counting library
+      homepage: https://github.com/dib-lab/khmer
+      documentation: https://khmer.readthedocs.io/en/latest/
+      tool_dev_url: https://github.com/dib-lab/khmer
+      doi: "10.12688/f1000research.6924.1"
+      licence: ["BSD License"]
+
+input:
+  - fasta:
+      type: file
+      description: fasta file
+      pattern: "*.{fa,fasta}"
+  - kmer_size:
+      type: value
+      description: k-mer size to use
+      pattern: "[0-9]+"
+
+output:
+  - report:
+      type: file
+      description: Text file containing unique-kmers.py execution report
+      pattern: "report.txt"
+  - kmers:
+      type: file
+      description: Text file containing number of kmers
+      pattern: "kmers.txt"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@kelly-sovacool"
diff --git a/tests/modules/CCBR/khmer/uniquekmers/main.nf b/tests/modules/CCBR/khmer/uniquekmers/main.nf
new file mode 100644
index 0000000..4dae054
--- /dev/null
+++ b/tests/modules/CCBR/khmer/uniquekmers/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { KHMER_UNIQUEKMERS } from '../../../../../modules/nf-core/khmer/uniquekmers/main.nf'
+
+workflow test_khmer_uniquekmers {
+
+    input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    KHMER_UNIQUEKMERS ( input, 50 )
+}
diff --git a/tests/modules/CCBR/khmer/uniquekmers/nextflow.config b/tests/modules/CCBR/khmer/uniquekmers/nextflow.config
new file mode 100644
index 0000000..8730f1c
--- /dev/null
+++ b/tests/modules/CCBR/khmer/uniquekmers/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/CCBR/khmer/uniquekmers/test.yml b/tests/modules/CCBR/khmer/uniquekmers/test.yml
new file mode 100644
index 0000000..ff5b12c
--- /dev/null
+++ b/tests/modules/CCBR/khmer/uniquekmers/test.yml
@@ -0,0 +1,10 @@
+- name: khmer uniquekmers test_khmer_uniquekmers
+  command: nextflow run ./tests/modules/nf-core/khmer/uniquekmers -entry test_khmer_uniquekmers -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/khmer/uniquekmers/nextflow.config
+  tags:
+    - khmer
+    - khmer/uniquekmers
+  files:
+    - path: output/khmer/kmers.txt
+      md5sum: 496ebf23653a01c7a42d743e47c19f65
+    - path: output/khmer/report.txt
+      md5sum: ee489abd3b244dea3640649e1790d55e

From aba489a356b45149952923dd17700557d05fcce6 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 10 Oct 2023 12:19:02 -0400
Subject: [PATCH 02/10] docs: link to original khmer module

---
 CHANGELOG.md | 3 ++-
 README.md    | 4 ++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1e3630c..b94fd13 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,7 @@
 ## development version
 
 - new modules:
-  - cutadapt
   - bwa/index
   - bwa/mem
+  - cutadapt
+  - khmer/uniquekmers
diff --git a/README.md b/README.md
index b007c64..cb9b173 100644
--- a/README.md
+++ b/README.md
@@ -37,6 +37,6 @@ Want to **contribute** to this project? Check out the [contributing guidelines](
 Many of the modules and subworkflows in this project reuse and adapt code from [nf-core/modules](https://github.com/nf-core/modules).
 In those cases, credit is noted in the `meta.yml` file of the module/subworkflow and also listed here:
 
+- [bwa](modules/CCBR/bwa) adapts the [nf-core bwa module](https://github.com/nf-core/chipseq/tree/51eba00b32885c4d0bec60db3cb0a45eb61e34c5/modules/nf-core/modules/bwa)
 - [cutadapt](modules/CCBR/cutadapt) adapts the [nf-core cutadapt module](https://github.com/nf-core/modules/tree/master/modules/nf-core/cutadapt)
-- [bwa_mem](modules/CCBR/bwa/mem) adapts the [nf-core bwa mem module](https://github.com/nf-core/chipseq/tree/51eba00b32885c4d0bec60db3cb0a45eb61e34c5/modules/nf-core/modules/bwa/mem)
-- [bwa_index](modules/CCBR/bwa/index) adapts the [nf-core bwa index module](https://github.com/nf-core/chipseq/tree/51eba00b32885c4d0bec60db3cb0a45eb61e34c5/modules/nf-core/modules/bwa/index)
+- [khmer](modules/CCBR/khmer) adapts the [nf-core khmer module](https://github.com/nf-core/modules/tree/b48a1efc8e067502e1a9bafbac788c1e0abdfc6a/modules/nf-core/khmer)

From 8a7ba9bfc875f8845f379f60e8718f6c04571072 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 10 Oct 2023 12:24:22 -0400
Subject: [PATCH 03/10] test: add khmer to tests/config/pytest_modules.yml

---
 tests/config/pytest_modules.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index f079ab3..cd8d2ca 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -9,3 +9,7 @@ bwa/mem:
 cutadapt:
   - modules/CCBR/cutadapt/**
   - tests/modules/CCBR/cutadapt/**
+
+khmer:
+  - modules/CCBR/khmer/**
+  - tests/CCBR/khmer/**

From aec48bb7122c177f5fec9f48f1d11ab751fe3898 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 10 Oct 2023 12:58:58 -0400
Subject: [PATCH 04/10] fix: repo name

---
 tests/modules/CCBR/khmer/uniquekmers/main.nf  | 2 +-
 tests/modules/CCBR/khmer/uniquekmers/test.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/modules/CCBR/khmer/uniquekmers/main.nf b/tests/modules/CCBR/khmer/uniquekmers/main.nf
index 4dae054..0a47792 100644
--- a/tests/modules/CCBR/khmer/uniquekmers/main.nf
+++ b/tests/modules/CCBR/khmer/uniquekmers/main.nf
@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { KHMER_UNIQUEKMERS } from '../../../../../modules/nf-core/khmer/uniquekmers/main.nf'
+include { KHMER_UNIQUEKMERS } from '../../../../../modules/CCBR/khmer/uniquekmers/main.nf'
 
 workflow test_khmer_uniquekmers {
 
diff --git a/tests/modules/CCBR/khmer/uniquekmers/test.yml b/tests/modules/CCBR/khmer/uniquekmers/test.yml
index ff5b12c..6f5216a 100644
--- a/tests/modules/CCBR/khmer/uniquekmers/test.yml
+++ b/tests/modules/CCBR/khmer/uniquekmers/test.yml
@@ -1,5 +1,5 @@
 - name: khmer uniquekmers test_khmer_uniquekmers
-  command: nextflow run ./tests/modules/nf-core/khmer/uniquekmers -entry test_khmer_uniquekmers -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/khmer/uniquekmers/nextflow.config
+  command: nextflow run ./tests/modules/CCBR/khmer/uniquekmers -entry test_khmer_uniquekmers -c ./tests/config/nextflow.config  -c ./tests/modules/CCBR/khmer/uniquekmers/nextflow.config
   tags:
     - khmer
     - khmer/uniquekmers

From ed2a90f230cb2a9a8094d6a1133269176aaf4ad1 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 10 Oct 2023 12:59:13 -0400
Subject: [PATCH 05/10] fix: khmer needs quay.io registry

---
 tests/modules/CCBR/khmer/uniquekmers/nextflow.config | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/modules/CCBR/khmer/uniquekmers/nextflow.config b/tests/modules/CCBR/khmer/uniquekmers/nextflow.config
index 8730f1c..f617d41 100644
--- a/tests/modules/CCBR/khmer/uniquekmers/nextflow.config
+++ b/tests/modules/CCBR/khmer/uniquekmers/nextflow.config
@@ -3,3 +3,5 @@ process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
 }
+
+docker.registry = 'quay.io'

From 3e6cc92fa14ef8512dd1436c5a7eee350e0f7b72 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 10 Oct 2023 14:06:28 -0400
Subject: [PATCH 06/10] fix: switch to ccbr custom container

---
 modules/CCBR/khmer/uniquekmers/main.nf | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/modules/CCBR/khmer/uniquekmers/main.nf b/modules/CCBR/khmer/uniquekmers/main.nf
index fca4d5c..f8b53e5 100644
--- a/modules/CCBR/khmer/uniquekmers/main.nf
+++ b/modules/CCBR/khmer/uniquekmers/main.nf
@@ -2,10 +2,7 @@ process KHMER_UNIQUEKMERS {
     tag "$fasta"
     label 'process_low'
 
-    conda "bioconda::khmer=3.0.0a3"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/khmer:3.0.0a3--py37haa7609a_2' :
-        'biocontainers/khmer:3.0.0a3--py37haa7609a_2' }"
+    container 'nciccbr/ccbr_khmer_3.0.0:v1'
 
     input:
     path fasta

From b5b4ba5c89b8a6d5fe117183d198616352fa465a Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 10 Oct 2023 14:12:50 -0400
Subject: [PATCH 07/10] fix: stub output

---
 modules/CCBR/khmer/uniquekmers/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/CCBR/khmer/uniquekmers/main.nf b/modules/CCBR/khmer/uniquekmers/main.nf
index f8b53e5..4413625 100644
--- a/modules/CCBR/khmer/uniquekmers/main.nf
+++ b/modules/CCBR/khmer/uniquekmers/main.nf
@@ -35,7 +35,7 @@ process KHMER_UNIQUEKMERS {
 
     stub:
     """
-    touch report.txt khmers.txt
+    touch report.txt kmers.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From bfc80f78d485951ae256157119adf7250e462536 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 10 Oct 2023 14:56:00 -0400
Subject: [PATCH 08/10] test: update khmer tests

PROFILE=docker nf-core modules create-test-yml khmer/uniquekmers --run-tests --force --no-prompts
---
 tests/modules/CCBR/khmer/uniquekmers/nextflow.config | 2 --
 tests/modules/CCBR/khmer/uniquekmers/test.yml        | 3 ++-
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/tests/modules/CCBR/khmer/uniquekmers/nextflow.config b/tests/modules/CCBR/khmer/uniquekmers/nextflow.config
index f617d41..8730f1c 100644
--- a/tests/modules/CCBR/khmer/uniquekmers/nextflow.config
+++ b/tests/modules/CCBR/khmer/uniquekmers/nextflow.config
@@ -3,5 +3,3 @@ process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
 }
-
-docker.registry = 'quay.io'
diff --git a/tests/modules/CCBR/khmer/uniquekmers/test.yml b/tests/modules/CCBR/khmer/uniquekmers/test.yml
index 6f5216a..c4f6ada 100644
--- a/tests/modules/CCBR/khmer/uniquekmers/test.yml
+++ b/tests/modules/CCBR/khmer/uniquekmers/test.yml
@@ -1,5 +1,5 @@
 - name: khmer uniquekmers test_khmer_uniquekmers
-  command: nextflow run ./tests/modules/CCBR/khmer/uniquekmers -entry test_khmer_uniquekmers -c ./tests/config/nextflow.config  -c ./tests/modules/CCBR/khmer/uniquekmers/nextflow.config
+  command: nextflow run ./tests/modules/CCBR/khmer/uniquekmers -entry test_khmer_uniquekmers -c ./tests/config/nextflow.config
   tags:
     - khmer
     - khmer/uniquekmers
@@ -8,3 +8,4 @@
       md5sum: 496ebf23653a01c7a42d743e47c19f65
     - path: output/khmer/report.txt
       md5sum: ee489abd3b244dea3640649e1790d55e
+    - path: output/khmer/versions.yml

From 6b923865d40f4b03aa252e213d8048fe1cbdba61 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 11 Oct 2023 09:19:53 -0400
Subject: [PATCH 09/10] fix: must specify exact module in config

---
 tests/config/pytest_modules.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index cd8d2ca..aa7c8c8 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -10,6 +10,6 @@ cutadapt:
   - modules/CCBR/cutadapt/**
   - tests/modules/CCBR/cutadapt/**
 
-khmer:
-  - modules/CCBR/khmer/**
-  - tests/CCBR/khmer/**
+khmer/uniquekmers:
+  - modules/CCBR/khmer/uniquekmers/**
+  - tests/CCBR/khmer/uniquekmers/**

From 89f8468b3633b364aaa62d4b1f958d22e681644d Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 11 Oct 2023 13:27:12 -0400
Subject: [PATCH 10/10] fix: khmer meta yaml - lint error from nf-core tools

---
 modules/CCBR/khmer/uniquekmers/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/CCBR/khmer/uniquekmers/meta.yml b/modules/CCBR/khmer/uniquekmers/meta.yml
index 5ffb451..3615902 100644
--- a/modules/CCBR/khmer/uniquekmers/meta.yml
+++ b/modules/CCBR/khmer/uniquekmers/meta.yml
@@ -20,7 +20,7 @@ input:
       description: fasta file
       pattern: "*.{fa,fasta}"
   - kmer_size:
-      type: value
+      type: integer
       description: k-mer size to use
       pattern: "[0-9]+"