Separate CI nexflow profile from test profile

TRON-Bioinformatics · Jun 14, 2024 · 2829297 · 2829297
1 parent 5c5041c
commit 2829297
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Showing 11 changed files with 21 additions and 16 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -6,12 +6,12 @@
  */
 
 profiles {
-  conda { params.enable_conda = true }
+  conda { 
+    params.enable_conda = true
+    conda.enabled = true
+  }
   debug { process.beforeScript = 'echo $HOSTNAME' }
-  test {
-    params.reference = "$baseDir/test_data/ucsc.hg19.minimal.fasta"
-    params.intervals = "$baseDir/test_data/intervals.minimal.bed"
-    params.gnomad = "$baseDir/test_data/gnomad.minimal.vcf.gz"
+  ci {
     params.memory_mutect2 = "2g"
     params.cpus_mutect2 = 1
     params.memory_read_orientation = "2g"
@@ -27,6 +27,11 @@ profiles {
     trace.enabled = false
     dag.enabled = false
   }
+  test {
+    params.reference = "$baseDir/test_data/ucsc.hg19.minimal.fasta"
+    params.intervals = "$baseDir/test_data/intervals.minimal.bed"
+    params.gnomad = "$baseDir/test_data/gnomad.minimal.vcf.gz"
+  }
 }
 
 // Export this variable to prevent local Python libraries from conflicting with those in the container

diff --git a/tests/test_01.sh b/tests/test_01.sh
@@ -5,6 +5,6 @@ source bin/assert.sh
 output=output/test1
 
 echo -e "sample_name\t"`pwd`"/test_data/SRR8244887.preprocessed.downsampled.bam\t"`pwd`"/test_data/SRR8244836.preprocessed.downsampled.bam" > test_data/test_input.txt
-nextflow main.nf -profile test,conda --output $output --input_files test_data/test_input.txt
+nextflow main.nf -profile test,conda,ci --output $output --input_files test_data/test_input.txt
 
 test -s $output/sample_name/sample_name.mutect2.vcf || { echo "Missing output VCF file!"; exit 1; }
diff --git a/tests/test_02.sh b/tests/test_02.sh
@@ -4,6 +4,6 @@
 source bin/assert.sh
 output=output/test2
 
-nextflow main.nf -profile test,conda --disable_common_germline_filter --output $output --input_files test_data/test_input.txt
+nextflow main.nf -profile test,conda,ci --disable_common_germline_filter --output $output --input_files test_data/test_input.txt
 
 test -s $output/sample_name/sample_name.mutect2.vcf || { echo "Missing output VCF file!"; exit 1; }
diff --git a/tests/test_03.sh b/tests/test_03.sh
@@ -5,6 +5,6 @@ source bin/assert.sh
 output=output/test3
 
 echo -e "sample_name_with_replicates\t"`pwd`"/test_data/SRR8244887.preprocessed.downsampled.bam,"`pwd`"/test_data/SRR8244887.preprocessed.downsampled.bam\t"`pwd`"/test_data/SRR8244836.preprocessed.downsampled.bam,"`pwd`"/test_data/SRR8244836.preprocessed.downsampled.bam" > test_data/test_input_with_replicates.txt
-nextflow main.nf -profile test,conda --input_files test_data/test_input_with_replicates.txt --output $output
+nextflow main.nf -profile test,conda,ci --input_files test_data/test_input_with_replicates.txt --output $output
 
 test -s $output/sample_name_with_replicates/sample_name_with_replicates.mutect2.vcf || { echo "Missing output VCF file!"; exit 1; }
diff --git a/tests/test_04.sh b/tests/test_04.sh
@@ -4,6 +4,6 @@
 source bin/assert.sh
 output=output/test4
 
-nextflow main.nf -profile test,conda --output $output --input_files test_data/test_input.txt --intervals false
+nextflow main.nf -profile test,conda,ci --output $output --input_files test_data/test_input.txt --intervals false
 
 test -s $output/sample_name/sample_name.mutect2.vcf || { echo "Missing output VCF file!"; exit 1; }
diff --git a/tests/test_05.sh b/tests/test_05.sh
@@ -9,7 +9,7 @@ output=output/test5
 echo -e "sample_name\t"`pwd`"/test_data/SRR8244887.preprocessed.downsampled.bam\t"`pwd`"/test_data/SRR8244836.preprocessed.downsampled.bam" > test_data/test_input.txt
 
 { # try
-    nextflow main.nf -profile test,conda --output $output --input_files test_data/test_input.txt &&
+    nextflow main.nf -profile test,conda,ci --output $output --input_files test_data/test_input.txt &&
     assert_true false "Error condition not captured"
 } || { # catch
     assert_true true

diff --git a/tests/test_06.sh b/tests/test_06.sh
@@ -10,15 +10,15 @@ output=output/test6
 
 echo -e "sample_name\t"`pwd`"/test_data/SRR8244887.preprocessed.downsampled.bam,"`pwd`"/test_data/SRR8244836.preprocessed.downsampled.bam\t"`pwd`"/test_data/SRR8244836.preprocessed.downsampled.bam" > test_data/test_input.txt
 { # try
-    nextflow main.nf -profile test,conda --output $output --input_files test_data/test_input.txt &&
+    nextflow main.nf -profile test,conda,ci --output $output --input_files test_data/test_input.txt &&
     assert_true false "Error condition not captured"
 } || { # catch
     assert_true true
 }
 
 echo -e "sample_name\t"`pwd`"/test_data/SRR8244887.preprocessed.downsampled.bam\t"`pwd`"/test_data/SRR8244887.preprocessed.downsampled.bam,"`pwd`"/test_data/SRR8244836.preprocessed.downsampled.bam" > test_data/test_input.txt
 { # try
-    nextflow main.nf -profile test,conda --output $output --input_files test_data/test_input.txt &&
+    nextflow main.nf -profile test,conda,ci --output $output --input_files test_data/test_input.txt &&
     assert_true false "Error condition not captured"
 } || { # catch
     assert_true true

diff --git a/tests/test_07.sh b/tests/test_07.sh
@@ -6,7 +6,7 @@ source bin/assert.sh
 output=output/test5
 
 echo -e "sample_name\t"`pwd`"/test_data/SRR8244887.preprocessed.downsampled.bam\t"`pwd`"/test_data/SRR8244836.preprocessed.downsampled.bam" > test_data/test_input.txt
-nextflow main.nf -profile test,conda --output $output --input_files test_data/test_input.txt \
+nextflow main.nf -profile test,conda,ci --output $output --input_files test_data/test_input.txt \
   --reference_version_funcotator hg19 \
   --funcotator /home/priesgo/funcotator/funcotator_dataSources.v1.7.20200521s
 

diff --git a/tests/test_08.sh b/tests/test_08.sh
@@ -5,7 +5,7 @@ source bin/assert.sh
 output=output/test8
 
 echo -e "sample_name\t"`pwd`"/test_data/SRR8244887.preprocessed.downsampled.bam\t"`pwd`"/test_data/SRR8244836.preprocessed.downsampled.bam" > test_data/test_input.txt
-nextflow main.nf -profile test,conda --output $output --input_files test_data/test_input.txt --enable_bam_output
+nextflow main.nf -profile test,conda,ci --output $output --input_files test_data/test_input.txt --enable_bam_output
 
 test -s $output/sample_name/sample_name.mutect2.vcf || { echo "Missing output VCF file!"; exit 1; }
 test -s $output/sample_name/sample_name.mutect2.assembled_haplotypes.bam || { echo "Missing output BAM file!"; exit 1; }

diff --git a/tests/test_09.sh b/tests/test_09.sh
@@ -5,6 +5,6 @@ source bin/assert.sh
 output=output/test9
 
 echo -e "sample_name\t"`pwd`"/test_data/SRR8244887.preprocessed.downsampled.bam\t"`pwd`"/test_data/SRR8244836.preprocessed.downsampled.bam" > test_data/test_input.txt
-nextflow main.nf -profile test,conda --output $output --input_files test_data/test_input.txt --gnomad false  --args_filter "--contamination-estimate 0.2"
+nextflow main.nf -profile test,conda,ci --output $output --input_files test_data/test_input.txt --gnomad false  --args_filter "--contamination-estimate 0.2"
 
 test -s $output/sample_name/sample_name.mutect2.vcf || { echo "Missing output VCF file!"; exit 1; }
diff --git a/tests/test_10.sh b/tests/test_10.sh
@@ -4,7 +4,7 @@
 source bin/assert.sh
 output=output/test10
 
-nextflow main.nf -profile test,conda --output $output \
+nextflow main.nf -profile test,conda,ci --output $output \
 --input_name sample_name \
 --input_tumor_bam `pwd`/test_data/SRR8244887.preprocessed.downsampled.bam \
 --input_normal_bam `pwd`/test_data/SRR8244836.preprocessed.downsampled.bam