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Merge nf-test into main #68

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fbf6e1f
init nf-test
AmstlerStephan Mar 7, 2024
3bb374f
add gitignore
AmstlerStephan Mar 7, 2024
64b6260
adapt config files to use nf-test
AmstlerStephan Mar 7, 2024
025ffa2
move test data
AmstlerStephan Mar 7, 2024
d6d0d43
adapt test.config
AmstlerStephan Mar 7, 2024
bb6b685
move testing data
AmstlerStephan Mar 7, 2024
4eabc2f
add data and tests for the cluster filtering and reformating
AmstlerStephan Mar 7, 2024
6a6ebb3
add further tests for reformat filter cluster
AmstlerStephan Mar 7, 2024
3b62f2b
add snapshot to test main workflow
AmstlerStephan Mar 7, 2024
a000151
no snapshots for workflows
AmstlerStephan Mar 7, 2024
3bf22c6
move testing data
AmstlerStephan Mar 7, 2024
9549bf7
Merge branch 'nf-test' of https://github.com/genepi/umi-pipeline-nf i…
AmstlerStephan Mar 7, 2024
8b471b3
adapt module structure
AmstlerStephan Mar 11, 2024
74543c6
adapt module paths in main workflow
AmstlerStephan Mar 11, 2024
adc32dc
add test data for variant calling
AmstlerStephan Mar 11, 2024
248918b
Add variant calling test data
AmstlerStephan Mar 11, 2024
5980ae9
Add test cases
AmstlerStephan Mar 11, 2024
1bd50f4
Add freebayes test cases
AmstlerStephan Mar 11, 2024
21bf952
Add tests for all variant callers
AmstlerStephan Mar 11, 2024
2fbbb8e
a
AmstlerStephan Mar 11, 2024
4dbee61
adapt lofreq parameters to have no minimal coverage
AmstlerStephan Mar 11, 2024
2f9aaf2
remove typo
AmstlerStephan Mar 11, 2024
170299f
Add fastq test files for merge input
AmstlerStephan Mar 12, 2024
1171cb7
Add tests and snapshot for merge_fastq
AmstlerStephan Mar 12, 2024
f7064c0
add test data for mapping
AmstlerStephan Mar 12, 2024
4ca53b9
add tests for consensus and final consensus reads
AmstlerStephan Mar 12, 2024
efe9a8e
Create test cases for split_reads
AmstlerStephan Mar 12, 2024
b4c843b
prepare tests for split reads process
AmstlerStephan Mar 15, 2024
36b8944
prepare tests for umi detection
AmstlerStephan Mar 15, 2024
b98af47
Add tests for clustering
AmstlerStephan Mar 15, 2024
6acd93d
remove params snippet
AmstlerStephan Mar 15, 2024
b19fc54
add tests for cluster polishing
AmstlerStephan Mar 15, 2024
0c2439f
add tests for cluster reformatting using
AmstlerStephan Mar 15, 2024
1521903
Add CI tests for nf-test
AmstlerStephan Jun 17, 2024
1cdef7b
Update ci-tests.yml
AmstlerStephan Jun 17, 2024
3077e99
Adapt docker file path
AmstlerStephan Jun 17, 2024
d2bf203
Merge branch 'nf-test' of https://github.com/genepi/umi-pipeline-nf i…
AmstlerStephan Jun 17, 2024
78c6dad
updated testing paramaters for faster execution
AmstlerStephan Jun 18, 2024
7f5d96e
Updated test cases
AmstlerStephan Jun 18, 2024
5b770cc
Updated local nf-test to v0.9.0 and updated snapshots
AmstlerStephan Jun 18, 2024
dccab02
Merge pull request #67 from genepi/main
AmstlerStephan Jun 18, 2024
b60ab80
specify minimap2 version
AmstlerStephan Jun 18, 2024
09ab258
test using existing release container
AmstlerStephan Jun 18, 2024
42f2b4b
remove docker initiation
AmstlerStephan Jun 18, 2024
8598c76
Temporarily remove snapshots of miniminap2
AmstlerStephan Jun 18, 2024
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adapt config files to use nf-test
AmstlerStephan committed Mar 7, 2024
commit 64b6260fd8fd6eddad7147d0124a8b01d4e9c81d
2 changes: 1 addition & 1 deletion config/base.config
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
// PROCESS RESOURCES
process {
withName: "POLISH_CLUSTER" {
memory = { 1.GB * task.attempt }
memory = { 2.GB * task.attempt }
cpus = 1
}

15 changes: 5 additions & 10 deletions nextflow.config
Original file line number Diff line number Diff line change
@@ -54,7 +54,7 @@ params {
medaka_model = "r1041_e82_400bps_hac_g615"
fwd_umi = "TTTVVVVTTVVVVTTVVVVTTVVVVTTT"
rev_umi = "AAABBBBAABBBBAABBBBAABBBBAAA"
adapter_length = 200
adapter_length = 100
min_length = 40
max_length = 60
minimap2_param = "-ax map-ont -k 13 --MD"
@@ -65,37 +65,32 @@ params {
// NEXTFLOW PROFILES

// Load base.config by default for all pipelines
includeConfig "${baseDir}/config/base.config"
includeConfig "config/base.config"

process.container = 'quay.io/genepi/umi-pipeline-nf:v0.2.0'

profiles {

// -profile conda
conda {
process.conda = "${baseDir}/env/environment.yml"
process.conda = "env/environment.yml"
}

// -profile docker
docker {
docker.enabled = true
}

// -profile singularity
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
}

// -profile test
test {
includeConfig "${baseDir}/config/test.config"
includeConfig "config/test.config"
}

// -profile custom
custom {
includeConfig "${baseDir}/config/custom.config"
includeConfig "config/custom.config"
}

}
2 changes: 1 addition & 1 deletion nf-test.config
Original file line number Diff line number Diff line change
@@ -3,6 +3,6 @@ config {
testsDir "tests"
workDir ".nf-test"
configFile "tests/nextflow.config"
profile ""
profile "test,docker"

}