Merge pull request nf-core#1426 from asp8200/fix_datapath_in_nftests

Fix datapath in nftests
asp8200 · Mar 1, 2024 · 355c354 · 355c354
2 parents ff1393d + ece0430
commit 355c354
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Showing 23 changed files with 345 additions and 711 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -26,6 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1408](https://github.com/nf-core/sarek/pull/1408), [#1412](https://github.com/nf-core/sarek/pull/1412) - Updating samtools to v1.19.2 - except in GATK/markduplicates. (Temporarily disabled nf-test for bwamem2/mem.)
 - [#1411](https://github.com/nf-core/sarek/pull/1411) - Temporarily disable sentieon related tests
 - [#1419](https://github.com/nf-core/sarek/pull/1419) - Updating GATK to v4.5, and updating samtools to v1.19.2 in GATK/markduplicates.
+- [#1426](https://github.com/nf-core/sarek/pull/1426) - Updating certain modules in order to fix the testdata-path in the nf-tests of those modules. Setting Docker runOptions for params.use_gatk_spark.
 - [#1428](https://github.com/nf-core/sarek/pull/1428) - Sync `TEMPLATE` with `tools` `2.13.1`
 
 ### Fixed

diff --git a/conf/test.config b/conf/test.config
@@ -108,6 +108,7 @@ if (System.getenv('PROFILE')) {
     } else if ("$PROFILE" == "docker") {
         conda.enabled                            = false
         docker.enabled                           = true
+        docker.runOptions                        = { params.use_gatk_spark ? '' : '-u $(id -u):$(id -g)' }.call()
         charliecloud.enabled                     = false
         podman.enabled                           = false
         shifter.enabled                          = false

diff --git a/conf/test/cache.config b/conf/test/cache.config
@@ -116,6 +116,7 @@ if (System.getenv('PROFILE')) {
     } else if ("$PROFILE" == "docker") {
         conda.enabled                            = false
         docker.enabled                           = true
+        docker.runOptions                        = { params.use_gatk_spark ? '' : '-u $(id -u):$(id -g)' }.call()
         charliecloud.enabled                     = false
         podman.enabled                           = false
         shifter.enabled                          = false

diff --git a/conf/test/use_gatk_spark.config b/conf/test/use_gatk_spark.config
@@ -14,3 +14,5 @@ params {
     use_gatk_spark = 'baserecalibrator,markduplicates'
     input          = "${projectDir}/tests/csv/3.0/fastq_tumor_only.csv"
 }
+
+docker.runOptions      = ''
diff --git a/modules.json b/modules.json
@@ -38,12 +38,12 @@
                     },
                     "bwa/index": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "6278bf9afd4a4b2d00fa6052250e73da3d91546f",
                         "installed_by": ["modules"]
                     },
                     "bwa/mem": {
                         "branch": "master",
-                        "git_sha": "ba3f3df395d2719dcef5c67189042a1dc555c701",
+                        "git_sha": "5908e575322666ccc33911a28b06e3f82260fe54",
                         "installed_by": ["modules"]
                     },
                     "bwamem2/index": {
@@ -58,12 +58,12 @@
                     },
                     "cat/cat": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8",
                         "installed_by": ["modules"]
                     },
                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "0997b47c93c06b49aa7b3fefda87e728312cf2ca",
                         "installed_by": ["modules"]
                     },
                     "cnvkit/antitarget": {
@@ -119,7 +119,7 @@
                     },
                     "dragmap/align": {
                         "branch": "master",
-                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
+                        "git_sha": "9a7efcec9b21baf1c67342faa6b8d905c972207f",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/dragmap/align/dragmap-align.diff"
                     },
@@ -171,7 +171,7 @@
                     },
                     "gatk4/applybqsr": {
                         "branch": "master",
-                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
+                        "git_sha": "af273ea6618c50e82c372abe18b0a225e84fe6f7",
                         "installed_by": ["modules"]
                     },
                     "gatk4/applyvqsr": {
@@ -181,7 +181,7 @@
                     },
                     "gatk4/baserecalibrator": {
                         "branch": "master",
-                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
+                        "git_sha": "8a223e11d4e6deb36484e01891eae9c1cacb5f5d",
                         "installed_by": ["modules"]
                     },
                     "gatk4/calculatecontamination": {
@@ -226,7 +226,7 @@
                     },
                     "gatk4/genomicsdbimport": {
                         "branch": "master",
-                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
+                        "git_sha": "194fca815cf594646e638fa5476acbcc296f1850",
                         "installed_by": ["modules"]
                     },
                     "gatk4/genotypegvcfs": {
@@ -256,7 +256,7 @@
                     },
                     "gatk4/markduplicates": {
                         "branch": "master",
-                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
+                        "git_sha": "194fca815cf594646e638fa5476acbcc296f1850",
                         "installed_by": ["modules"]
                     },
                     "gatk4/mergemutectstats": {
@@ -266,7 +266,7 @@
                     },
                     "gatk4/mergevcfs": {
                         "branch": "master",
-                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
+                        "git_sha": "194fca815cf594646e638fa5476acbcc296f1850",
                         "installed_by": ["modules"]
                     },
                     "gatk4/mutect2": {
@@ -466,7 +466,7 @@
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620",
                         "installed_by": ["modules"]
                     },
                     "unzip": {

diff --git a/modules/nf-core/bwa/index/tests/main.nf.test b/modules/nf-core/bwa/index/tests/main.nf.test
diff --git a/modules/nf-core/bwa/mem/tests/main.nf.test b/modules/nf-core/bwa/mem/tests/main.nf.test
diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf
diff --git a/modules/nf-core/cat/cat/tests/main.nf.test b/modules/nf-core/cat/cat/tests/main.nf.test
diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml
diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf