From f1fc7fc38eb65782cdf2d05bc4d56a11ec8922a8 Mon Sep 17 00:00:00 2001
From: jvhagey <qpk9@cdc.gov>
Date: Tue, 24 May 2022 15:15:07 -0400
Subject: [PATCH 1/4] adding upzip

---
 modules/gamma/{ => gamma}/main.nf             | 15 ++++++++--
 modules/gamma/{ => gamma}/meta.yml            |  0
 tests/modules/gamma/gamma/main.nf             | 29 +++++++++++++++++++
 .../modules/gamma/{ => gamma}/nextflow.config |  0
 tests/modules/gamma/gamma/test.yml            | 29 +++++++++++++++++++
 tests/modules/gamma/main.nf                   | 17 -----------
 tests/modules/gamma/test.yml                  | 13 ---------
 7 files changed, 71 insertions(+), 32 deletions(-)
 rename modules/gamma/{ => gamma}/main.nf (83%)
 rename modules/gamma/{ => gamma}/meta.yml (100%)
 create mode 100644 tests/modules/gamma/gamma/main.nf
 rename tests/modules/gamma/{ => gamma}/nextflow.config (100%)
 create mode 100644 tests/modules/gamma/gamma/test.yml
 delete mode 100644 tests/modules/gamma/main.nf
 delete mode 100644 tests/modules/gamma/test.yml

diff --git a/modules/gamma/main.nf b/modules/gamma/gamma/main.nf
similarity index 83%
rename from modules/gamma/main.nf
rename to modules/gamma/gamma/main.nf
index e176ee68..51a5f6c8 100644
--- a/modules/gamma/main.nf
+++ b/modules/gamma/gamma/main.nf
@@ -26,13 +26,24 @@ process GAMMA {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+
     """
-    GAMMA.py \\
+    if [[ ${fasta} == *.gz ]]
+    then
+        FNAME=\$(basename ${fasta} .gz)
+        gunzip -f ${fasta}
+        GAMMA.py \\
+        $args \\
+        "\${FNAME}" \\
+        $db \\
+        $prefix
+    else
+        GAMMA.py \\
         $args \\
         $fasta \\
         $db \\
         $prefix
-
+    fi
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         gamma: $VERSION
diff --git a/modules/gamma/meta.yml b/modules/gamma/gamma/meta.yml
similarity index 100%
rename from modules/gamma/meta.yml
rename to modules/gamma/gamma/meta.yml
diff --git a/tests/modules/gamma/gamma/main.nf b/tests/modules/gamma/gamma/main.nf
new file mode 100644
index 00000000..070a3bf1
--- /dev/null
+++ b/tests/modules/gamma/gamma/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GAMMA } from '../../../../modules/gamma/gamma/main.nf'
+
+workflow test_unzip {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true),
+    ]
+
+    db = [ file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/ResGANNCBI_20210507_srst2.fasta", checkIfExists: true), ]
+
+    GAMMA ( input, db )
+}
+
+workflow test_gamma {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    db = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+
+    GAMMA ( input, db )
+}
diff --git a/tests/modules/gamma/nextflow.config b/tests/modules/gamma/gamma/nextflow.config
similarity index 100%
rename from tests/modules/gamma/nextflow.config
rename to tests/modules/gamma/gamma/nextflow.config
diff --git a/tests/modules/gamma/gamma/test.yml b/tests/modules/gamma/gamma/test.yml
new file mode 100644
index 00000000..308d890f
--- /dev/null
+++ b/tests/modules/gamma/gamma/test.yml
@@ -0,0 +1,29 @@
+- name: gamma gamma test_unzip
+  command: nextflow run tests/modules/gamma/gamma -entry test_unzip -c tests/config/nextflow.config
+  tags:
+    - gamma/gamma
+    - gamma
+  files:
+    - path: /tmp/tmppm1ybfln/gamma/test.fasta
+      md5sum: 5b3b831d863fffaa3410a9ee7bfa12ce
+    - path: /tmp/tmppm1ybfln/gamma/test.gamma
+      md5sum: 46165a89e10b7315d3a9b0aa6c561626
+    - path: /tmp/tmppm1ybfln/gamma/test.psl
+      md5sum: f489ce4602ddbcb692d5781ee3fbf449
+    - path: /tmp/tmppm1ybfln/gamma/versions.yml
+      md5sum: ad23c3ec60663598543cbe8bc74bc4ab
+
+- name: gamma gamma test_gamma
+  command: nextflow run tests/modules/gamma/gamma -entry test_gamma -c tests/config/nextflow.config
+  tags:
+    - gamma/gamma
+    - gamma
+  files:
+    - path: /tmp/tmpw3chm6da/gamma/test.fasta
+      md5sum: df37b48466181311e0a679f3c5878484
+    - path: /tmp/tmpw3chm6da/gamma/test.gamma
+      md5sum: 3256708fa517a65ed01d99e0e3c762ae
+    - path: /tmp/tmpw3chm6da/gamma/test.psl
+      md5sum: 162a2757ed3b167ae1e0cdb24213f940
+    - path: /tmp/tmpw3chm6da/gamma/versions.yml
+      md5sum: 3fefb5b46c94993362243c5f9a472057
diff --git a/tests/modules/gamma/main.nf b/tests/modules/gamma/main.nf
deleted file mode 100644
index f9477706..00000000
--- a/tests/modules/gamma/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GAMMA } from '../../../modules/gamma/main.nf'
-
-workflow test_gamma {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    db = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
-
-    GAMMA ( input, db )
-}
diff --git a/tests/modules/gamma/test.yml b/tests/modules/gamma/test.yml
deleted file mode 100644
index 1b493b49..00000000
--- a/tests/modules/gamma/test.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-- name: gamma test_gamma
-  command: nextflow run tests/modules/gamma -entry test_gamma -c tests/config/nextflow.config
-  tags:
-    - gamma
-  files:
-    - path: output/gamma/test.fasta
-      md5sum: df37b48466181311e0a679f3c5878484
-    - path: output/gamma/test.gamma
-      md5sum: 3256708fa517a65ed01d99e0e3c762ae
-    - path: output/gamma/test.psl
-      md5sum: 162a2757ed3b167ae1e0cdb24213f940
-    - path: output/gamma/versions.yml
-      md5sum: 3fefb5b46c94993362243c5f9a472057

From b8aaea7429e74cb23acff21b03ba3814d7905ed1 Mon Sep 17 00:00:00 2001
From: jvhagey <qpk9@cdc.gov>
Date: Tue, 24 May 2022 16:27:00 -0400
Subject: [PATCH 2/4] updating paths in test.yml

---
 modules/gamma/gamma/main.nf        |  2 +-
 modules/gamma/gamma/meta.yml       |  3 ++-
 tests/modules/gamma/gamma/main.nf  |  6 +++---
 tests/modules/gamma/gamma/test.yml | 20 ++++++++++----------
 4 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/modules/gamma/gamma/main.nf b/modules/gamma/gamma/main.nf
index 51a5f6c8..fddced62 100644
--- a/modules/gamma/gamma/main.nf
+++ b/modules/gamma/gamma/main.nf
@@ -1,6 +1,6 @@
 def VERSION = '2.1' // Version information not provided by tool on CLI
 
-process GAMMA {
+process GAMMA_GAMMA {
     tag "$meta.id"
     label 'process_low'
 
diff --git a/modules/gamma/gamma/meta.yml b/modules/gamma/gamma/meta.yml
index 316b685b..d9e272e2 100644
--- a/modules/gamma/gamma/meta.yml
+++ b/modules/gamma/gamma/meta.yml
@@ -1,4 +1,4 @@
-name: "gamma"
+name: "gamma_gamma"
 description: Gene Allele Mutation Microbial Assessment
 keywords:
   - gamma
@@ -61,3 +61,4 @@ output:
 authors:
   - "@sateeshperi"
   - "@rastanton"
+  - "@jvhagey"
diff --git a/tests/modules/gamma/gamma/main.nf b/tests/modules/gamma/gamma/main.nf
index 070a3bf1..97e58be7 100644
--- a/tests/modules/gamma/gamma/main.nf
+++ b/tests/modules/gamma/gamma/main.nf
@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { GAMMA } from '../../../../modules/gamma/gamma/main.nf'
+include { GAMMA_GAMMA } from '../../../../modules/gamma/gamma/main.nf'
 
 workflow test_unzip {
 
@@ -13,7 +13,7 @@ workflow test_unzip {
 
     db = [ file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/ResGANNCBI_20210507_srst2.fasta", checkIfExists: true), ]
 
-    GAMMA ( input, db )
+    GAMMA_GAMMA ( input, db )
 }
 
 workflow test_gamma {
@@ -25,5 +25,5 @@ workflow test_gamma {
 
     db = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
 
-    GAMMA ( input, db )
+    GAMMA_GAMMA ( input, db )
 }
diff --git a/tests/modules/gamma/gamma/test.yml b/tests/modules/gamma/gamma/test.yml
index 308d890f..2c649105 100644
--- a/tests/modules/gamma/gamma/test.yml
+++ b/tests/modules/gamma/gamma/test.yml
@@ -4,14 +4,14 @@
     - gamma/gamma
     - gamma
   files:
-    - path: /tmp/tmppm1ybfln/gamma/test.fasta
+    - path: output/gamma/gamma/test.fasta
       md5sum: 5b3b831d863fffaa3410a9ee7bfa12ce
-    - path: /tmp/tmppm1ybfln/gamma/test.gamma
+    - path: output/gamma/gamma/test.gamma
       md5sum: 46165a89e10b7315d3a9b0aa6c561626
-    - path: /tmp/tmppm1ybfln/gamma/test.psl
+    - path: output/gamma/gamma/test.psl
       md5sum: f489ce4602ddbcb692d5781ee3fbf449
-    - path: /tmp/tmppm1ybfln/gamma/versions.yml
-      md5sum: ad23c3ec60663598543cbe8bc74bc4ab
+    - path: output/gamma/gamma/versions.yml
+      md5sum: 8baafec7b3b87f788f69e30d317c9722
 
 - name: gamma gamma test_gamma
   command: nextflow run tests/modules/gamma/gamma -entry test_gamma -c tests/config/nextflow.config
@@ -19,11 +19,11 @@
     - gamma/gamma
     - gamma
   files:
-    - path: /tmp/tmpw3chm6da/gamma/test.fasta
+    - path: output/gamma/gamma/test.fasta
       md5sum: df37b48466181311e0a679f3c5878484
-    - path: /tmp/tmpw3chm6da/gamma/test.gamma
+    - path: output/gamma/gamma/test.gamma
       md5sum: 3256708fa517a65ed01d99e0e3c762ae
-    - path: /tmp/tmpw3chm6da/gamma/test.psl
+    - path: output/gamma/gamma/test.psl
       md5sum: 162a2757ed3b167ae1e0cdb24213f940
-    - path: /tmp/tmpw3chm6da/gamma/versions.yml
-      md5sum: 3fefb5b46c94993362243c5f9a472057
+    - path: output/gamma/gamma/versions.yml
+      md5sum: b75c2871d8cac2f8ac67c0fbd22babd6

From bb999395aa4d03d02336794c655cfcdf34855b05 Mon Sep 17 00:00:00 2001
From: jvhagey <qpk9@cdc.gov>
Date: Tue, 24 May 2022 19:19:38 -0400
Subject: [PATCH 3/4] fixed pytest_modules.yml

---
 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 2063d691..80711bae 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -707,9 +707,9 @@ freebayes:
   - modules/freebayes/**
   - tests/modules/freebayes/**
 
-gamma:
-  - modules/gamma/**
-  - tests/modules/gamma/**
+gamma/gamma:
+  - modules/gamma/gamma/**
+  - tests/modules/gamma/gamma/**
 
 gatk4/applybqsr:
   - modules/gatk4/applybqsr/**

From 127665d27ba5512bfe1596f86c2b11a197556233 Mon Sep 17 00:00:00 2001
From: jvhagey <qpk9@cdc.gov>
Date: Tue, 24 May 2022 19:27:09 -0400
Subject: [PATCH 4/4] fixed test.yml

---
 tests/modules/gamma/gamma/test.yml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/tests/modules/gamma/gamma/test.yml b/tests/modules/gamma/gamma/test.yml
index 2c649105..163eda5f 100644
--- a/tests/modules/gamma/gamma/test.yml
+++ b/tests/modules/gamma/gamma/test.yml
@@ -4,13 +4,13 @@
     - gamma/gamma
     - gamma
   files:
-    - path: output/gamma/gamma/test.fasta
+    - path: output/gamma/test.fasta
       md5sum: 5b3b831d863fffaa3410a9ee7bfa12ce
-    - path: output/gamma/gamma/test.gamma
+    - path: output/gamma/test.gamma
       md5sum: 46165a89e10b7315d3a9b0aa6c561626
-    - path: output/gamma/gamma/test.psl
+    - path: output/gamma/test.psl
       md5sum: f489ce4602ddbcb692d5781ee3fbf449
-    - path: output/gamma/gamma/versions.yml
+    - path: output/gamma/versions.yml
       md5sum: 8baafec7b3b87f788f69e30d317c9722
 
 - name: gamma gamma test_gamma
@@ -19,11 +19,11 @@
     - gamma/gamma
     - gamma
   files:
-    - path: output/gamma/gamma/test.fasta
+    - path: output/gamma/test.fasta
       md5sum: df37b48466181311e0a679f3c5878484
-    - path: output/gamma/gamma/test.gamma
+    - path: output/gamma/test.gamma
       md5sum: 3256708fa517a65ed01d99e0e3c762ae
-    - path: output/gamma/gamma/test.psl
+    - path: output/gamma/test.psl
       md5sum: 162a2757ed3b167ae1e0cdb24213f940
-    - path: output/gamma/gamma/versions.yml
+    - path: output/gamma/versions.yml
       md5sum: b75c2871d8cac2f8ac67c0fbd22babd6