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TRON-Bioinformatics · May 23, 2024 · 5538ef9 · 5538ef9
1 parent 173ff84
commit 5538ef9
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Showing 14 changed files with 18 additions and 16 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -26,16 +26,18 @@ profiles {
     conda.useMamba = true
   }
   debug { process.beforeScript = 'echo $HOSTNAME' }
-  test {
-    params.input_files = "test_data/test_input_paired.txt"
-    params.reference = "$baseDir/test_data/ucsc.hg19.minimal.fasta"
+  ci {
     params.cpus = 1
     params.memory = "3g"
     timeline.enabled = false
     report.enabled = false
     trace.enabled = false
     dag.enabled = false
   }
+  test {
+    params.input_files = "test_data/test_input_paired.txt"
+    params.reference = "$baseDir/test_data/ucsc.hg19.minimal.fasta"
+  }
 }
 
 // Export this variable to prevent local Python libraries from conflicting with those in the container

diff --git a/tests/run_test_1.sh b/tests/run_test_1.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test1
-nextflow main.nf -profile test,conda --output $output_folder
+nextflow main.nf -profile test,conda,ci --output $output_folder
 test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 1 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 1 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.fastp_stats.html || { echo "Missing test 1 output file!"; exit 1; }

diff --git a/tests/run_test_10.sh b/tests/run_test_10.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test10
-nextflow main.nf -profile test,conda --library single --algorithm mem2 --output $output_folder
+nextflow main.nf -profile test,conda,ci --library single --algorithm mem2 --output $output_folder
 test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 3 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 3 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.fastp_stats.html || { echo "Missing test 3 output file!"; exit 1; }

diff --git a/tests/run_test_11.sh b/tests/run_test_11.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test11
-nextflow main.nf -profile test,conda --algorithm star --reference `pwd`/test_data --output $output_folder
+nextflow main.nf -profile test,conda,ci --algorithm star --reference `pwd`/test_data --output $output_folder
 test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 4 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 4 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.fastp_stats.html || { echo "Missing test 4 output file!"; exit 1; }

diff --git a/tests/run_test_12.sh b/tests/run_test_12.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test12
-nextflow main.nf -profile test,conda --algorithm star --library single --reference `pwd`/test_data --output $output_folder
+nextflow main.nf -profile test,conda,ci --algorithm star --library single --reference `pwd`/test_data --output $output_folder
 test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 4 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 4 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.fastp_stats.html || { echo "Missing test 4 output file!"; exit 1; }

diff --git a/tests/run_test_13.sh b/tests/run_test_13.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test13
-nextflow main.nf -profile test,conda --algorithm star --star_two_pass_mode --reference `pwd`/test_data --output $output_folder
+nextflow main.nf -profile test,conda,ci --algorithm star --star_two_pass_mode --reference `pwd`/test_data --output $output_folder
 test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 4 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 4 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.fastp_stats.html || { echo "Missing test 4 output file!"; exit 1; }

diff --git a/tests/run_test_2.sh b/tests/run_test_2.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test2
-nextflow main.nf -profile test,conda --inception --output $output_folder
+nextflow main.nf -profile test,conda,ci --inception --output $output_folder
 test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 2 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 2 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.fastp_stats.html || { echo "Missing test 2 output file!"; exit 1; }

diff --git a/tests/run_test_3.sh b/tests/run_test_3.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test3
-nextflow main.nf -profile test,conda --library single --output $output_folder
+nextflow main.nf -profile test,conda,ci --library single --output $output_folder
 test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 3 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 3 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.fastp_stats.html || { echo "Missing test 3 output file!"; exit 1; }

diff --git a/tests/run_test_4.sh b/tests/run_test_4.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test4
-nextflow main.nf -profile test,conda --algorithm mem --output $output_folder
+nextflow main.nf -profile test,conda,ci --algorithm mem --output $output_folder
 test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 4 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 4 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.fastp_stats.html || { echo "Missing test 4 output file!"; exit 1; }

diff --git a/tests/run_test_5.sh b/tests/run_test_5.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test5
-nextflow main.nf -profile test,conda --algorithm mem --library single --output $output_folder
+nextflow main.nf -profile test,conda,ci --algorithm mem --library single --output $output_folder
 test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 5 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 5 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.fastp_stats.html || { echo "Missing test 5 output file!"; exit 1; }

diff --git a/tests/run_test_6.sh b/tests/run_test_6.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test6
-nextflow main.nf -profile test,conda --output $output_folder --input_files false \
+nextflow main.nf -profile test,conda,ci --output $output_folder --input_files false \
 --input_fastq1 test_data/TESTX_S1_L001_R1_001.fastq.gz \
 --input_fastq2 test_data/TESTX_S1_L001_R2_001.fastq.gz --input_name test
 test -s $output_folder/test.bam || { echo "Missing test 6 output file!"; exit 1; }

diff --git a/tests/run_test_7.sh b/tests/run_test_7.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test7
-nextflow main.nf -profile test,conda --output $output_folder --input_files false \
+nextflow main.nf -profile test,conda,ci --output $output_folder --input_files false \
 --input_fastq1 test_data/TESTX_S1_L001_R1_001.fastq.gz \
 --library single --input_name test
 test -s $output_folder/test.bam || { echo "Missing test 7 output file!"; exit 1; }

diff --git a/tests/run_test_8.sh b/tests/run_test_8.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test8
-nextflow main.nf -profile test,conda --algorithm mem --skip_trimming --output $output_folder
+nextflow main.nf -profile test,conda,ci --algorithm mem --skip_trimming --output $output_folder
 test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 8 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 8 output file!"; exit 1; }
 if [ -f $output_folder/TESTX_S1_L001.fastp_stats.html ]; then

diff --git a/tests/run_test_9.sh b/tests/run_test_9.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test9
-nextflow main.nf -profile test,conda --algorithm mem2 --output $output_folder
+nextflow main.nf -profile test,conda,ci --algorithm mem2 --output $output_folder
 test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 4 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 4 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.fastp_stats.html || { echo "Missing test 4 output file!"; exit 1; }