Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update filter_query module to accommodate multiple queries #14

Merged
merged 6 commits into from
Jun 12, 2024
Merged
Changes from 1 commit
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Changed cluster_file output filename for clarity
kylacochrane committed Jun 12, 2024
commit 15b7090691f90dbb969be9db01218715673201ca
4 changes: 2 additions & 2 deletions modules/local/cluster_file/main.nf
Original file line number Diff line number Diff line change
@@ -6,7 +6,7 @@ process CLUSTER_FILE {
val meta

output:
path("expected_clusters.txt"), emit: text
path("reference_clusters.txt"), emit: text

exec:
def outputLines = []
@@ -37,7 +37,7 @@ process CLUSTER_FILE {
}

// Write the text file, iterating over each sample
task.workDir.resolve("expected_clusters.txt").withWriter { writer ->
task.workDir.resolve("reference_clusters.txt").withWriter { writer ->
outputLines.each { line ->
writer.writeLine(line)
}
4 changes: 2 additions & 2 deletions tests/modules/cluster_file/main.nf.test
Original file line number Diff line number Diff line change
@@ -25,8 +25,8 @@ nextflow_process {
assert process.success
assert path("$launchDir/cluster_results").exists()

// Check expected_clusters
def actual_clusters = path("$launchDir/cluster_results/cluster/expected_clusters.txt")
// Check reference_clusters file
def actual_clusters = path("$launchDir/cluster_results/cluster/reference_clusters.txt")
def expected_clusters = path("$baseDir/tests/data/clusters/expected_clusters.txt")
assert actual_clusters.text == expected_clusters.text
}
4 changes: 2 additions & 2 deletions tests/pipelines/main.nf.test
Original file line number Diff line number Diff line change
@@ -33,7 +33,7 @@ nextflow_pipeline {
assert actual_distances.text == expected_distances.text

// Verify cluster file
def actual_cluster = path("$launchDir/results/cluster/expected_clusters.txt")
def actual_cluster = path("$launchDir/results/cluster/reference_clusters.txt")
def expected_cluster = path("$baseDir/tests/data/clusters/expected_clusters.txt")
assert actual_cluster.text == expected_cluster.text

@@ -84,7 +84,7 @@ nextflow_pipeline {
assert actual_distances.text == expected_distances.text

// Verify cluster file
def actual_cluster = path("$launchDir/results/cluster/expected_clusters.txt")
def actual_cluster = path("$launchDir/results/cluster/reference_clusters.txt")
def expected_cluster = path("$baseDir/tests/data/clusters/expected_clusters.txt")
assert actual_cluster.text == expected_cluster.text