Adapt tests to sage/msgf - runs fine locally

lehtiolab · Jan 31, 2025 · 5f14dc9 · 5f14dc9
1 parent 197f1d4
commit 5f14dc9
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Showing 11 changed files with 52 additions and 33 deletions.
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -10,13 +10,21 @@ jobs:
   create-container:
     uses: ./.github/workflows/container.yml
 
-  run-all-tests:
+  run-all-tests-sage:
     needs: create-container
+    env:
+      SEARCH: sage
+    uses: ./.github/workflows/tests_all.yml
+
+  run-all-tests-msgf:
+    needs: create-container
+    env:
+      SEARCH: msgf
     uses: ./.github/workflows/tests_all.yml
 
   create-release:  
     runs-on: ubuntu-latest
-    needs: run-all-tests
+    needs: [run-all-tests-sage, run-all-tests-msgf]
     steps:
       - uses: ncipollo/release-action@v1
         with:

diff --git a/.github/workflows/single_test.yml b/.github/workflows/single_test.yml
@@ -20,4 +20,4 @@ jobs:
             uses: nf-core/setup-nextflow@v2
 
           - name: Run single test
-            run: bash run_tests.sh tmt16_fast
+            run: bash run_tests.sh sage tmt16_fast
diff --git a/.github/workflows/tests_all.yml b/.github/workflows/tests_all.yml
@@ -15,7 +15,7 @@ jobs:
             uses: nf-core/setup-nextflow@v2
 
           - name: Run tests
-            run: bash run_tests.sh tmt16
+            run: bash run_tests.sh $SEARCH tmt16
 
     test-tmt18:
         runs-on: ubuntu-latest
@@ -27,7 +27,7 @@ jobs:
             uses: nf-core/setup-nextflow@v2
 
           - name: Run tests
-            run: bash run_tests.sh tmt18
+            run: bash run_tests.sh $SEARCH tmt18
 
     test-labelfree:
         runs-on: ubuntu-latest
@@ -39,7 +39,7 @@ jobs:
             uses: nf-core/setup-nextflow@v2
 
           - name: Run tests
-            run: bash run_tests.sh labelfree
+            run: bash run_tests.sh $SEARCH labelfree
 
     test-lf_phos:
         runs-on: ubuntu-latest
@@ -51,7 +51,7 @@ jobs:
             uses: nf-core/setup-nextflow@v2
 
           - name: Run tests
-            run: bash run_tests.sh labelfree_phos
+            run: bash run_tests.sh $SEARCH labelfree_phos
 
     test-tims:
         runs-on: ubuntu-latest
@@ -63,7 +63,7 @@ jobs:
             uses: nf-core/setup-nextflow@v2
 
           - name: Run tests
-            run: bash run_tests.sh tims
+            run: bash run_tests.sh $SEARCH tims
 
     test-mixed-tmt:
         runs-on: ubuntu-latest
@@ -75,4 +75,4 @@ jobs:
             uses: nf-core/setup-nextflow@v2
 
           - name: Run tests
-            run: bash run_tests.sh tmt16_18
+            run: bash run_tests.sh $SEARCH tmt16_18
diff --git a/run_tests.sh b/run_tests.sh
@@ -11,6 +11,12 @@ rundir=$(pwd)
 export repodir=$(dirname "$(realpath -s "$0")")
 export testdir="${repodir}/tests/"
 export testdata="${rundir}/static-resources/test-data/ddamsproteomics"
+if [ "$1" != 'sage' ] && [ "$1" != 'msgf' ]
+then
+	echo 'Must run tests with "bash run_tests.sh sage [or msgf]"'
+	exit 1
+fi
+export NXFCMD="nextflow run -resume -profile test ${repodir}/main.nf --$1"
 
 if [ -e "${testdata}" ]
 then
@@ -33,7 +39,8 @@ test_names=(
     tims
 )
 
-if [ -z "$1" ]
+
+if [ -z "$2" ]
 then
 	# Run all tests, do not exit with failures
 	# Manual runs
@@ -54,12 +61,12 @@ then
 else
 	# Single test, exit with error when failing
 	# Used in github actions
-       	bash "${testdir}/$1.sh"
+       	bash "${testdir}/$2.sh"
        	if [[ "$?" == 0 ]]
        	then
-	       	echo ${green}"$1" - SUCCESS ${reset}
+	       	echo ${green}"$2" - SUCCESS ${reset}
        	else
-	       	echo ${red}"$1" - FAIL ${reset}
+	       	echo ${red}"$2" - FAIL ${reset}
 		exit 1
        	fi
 fi
diff --git a/tests/labelfree.sh b/tests/labelfree.sh
@@ -5,7 +5,7 @@ set -eu
 echo Normal labelfree test
 name=lf
 cat ${testdir}/lf_mzmls.txt | envsubst > test_output/mzmldef
-nextflow run -resume -profile test ${repodir}/main.nf --name ${name} \
+$NXFCMD --name ${name} \
     --outdir test_output/${name} \
     --input test_output/mzmldef \
     --genes \
@@ -23,7 +23,7 @@ nextflow run -resume -profile test ${repodir}/main.nf --name ${name} \
 echo Labelfree run with warnings: no decoy in setB, no target in setA
 name=lf_notarget
 cat ${testdir}/lf_mzmls.txt | envsubst > test_output/mzmldef
-nextflow run -resume -profile test ${repodir}/main.nf --name ${name} \
+$NXFCMD --name ${name} \
     --outdir test_output/${name} \
     --input test_output/mzmldef \
     --genes \
@@ -34,7 +34,7 @@ nextflow run -resume -profile test ${repodir}/main.nf --name ${name} \
 echo Labelfree run without fractions, with warnings: no decoy in setB, no target in setA
 name=lf_nofrac_notarget
 cat ${testdir}/lf_mzmls_nofrac.txt | envsubst > test_output/mzmldef
-nextflow run -resume -profile test ${repodir}/main.nf --name ${name} \
+$NXFCMD --name ${name} \
     --outdir test_output/${name} \
     --input test_output/mzmldef \
     --genes \
@@ -46,7 +46,7 @@ nextflow run -resume -profile test ${repodir}/main.nf --name ${name} \
 echo Single file labelfree test
 name=lf_singlefile
 cat <(head -n1 ${testdir}/lf_mzmls.txt) <(grep setA ${testdir}/lf_mzmls.txt) | envsubst > test_output/mzmldef
-nextflow run -resume -profile test ${repodir}/main.nf --name ${name} \
+$NXFCMD --name ${name} \
     --outdir test_output/${name} \
     --input test_output/mzmldef \
     --genes \

diff --git a/tests/labelfree_phos.sh b/tests/labelfree_phos.sh
@@ -5,7 +5,7 @@ echo Phospho, labelfree, one luciphor setB not enough PSMs
 name=labelfree_phos
 lfphos_dir=test_output/${name}
 cat ${testdir}/lf_mzmls.txt | envsubst > test_output/mzmldef
-nextflow run -resume -profile test ${repodir}/main.nf --name ${name} \
+$NXFCMD --name ${name} \
     --outdir ${lfphos_dir} \
     --input test_output/mzmldef \
     --genes \
@@ -19,7 +19,7 @@ nextflow run -resume -profile test ${repodir}/main.nf --name ${name} \
 # LF phos where we add replace a set with a "new" set
 name=labelfree_phos_addset
 cat <(head -n1 ${testdir}/lf_mzmls.txt) <(grep setA ${testdir}/lf_mzmls.txt) | envsubst > test_output/mzmldef
-nextflow run -resume -profile test ${repodir}/main.nf --name ${name} \
+$NXFCMD --name ${name} \
     --outdir test_output/${name} \
     --input test_output/mzmldef \
     --oldmzmldef ${testdir}/lf_mzmls.txt \
@@ -41,7 +41,7 @@ nextflow run -resume -profile test ${repodir}/main.nf --name ${name} \
 echo LF phos no decoy
 name=labelfree_phos_nodecoy
 cat <(head -n1 ${testdir}/lf_mzmls.txt) <(grep setA ${testdir}/lf_mzmls.txt) | envsubst > test_output/mzmldef
-nextflow run -resume -profile test ${repodir}/main.nf --name ${name} \
+$NXFCMD --name ${name} \
     --outdir test_output/${name} \
     --input test_output/mzmldef \
     --genes \
@@ -55,9 +55,10 @@ set +eu
 echo Run in which no target PSMs are found - crashes
 name=labelfree_phos_notarget
 cat <(head -n1 ${testdir}/lf_mzmls.txt) <(grep setA ${testdir}/lf_mzmls.txt) | envsubst > test_output/mzmldef
-nextflow run -resume -profile test ${repodir}/main.nf --name ${name} \
+$NXFCMD --name ${name} \
     --outdir test_output/${name} \
     --input test_output/mzmldef \
+    --psmconflvl 0.001 \
     --genes \
     --tdb ${testdata}/lf.fa \
     --mods 'carbamidomethyl;oxidation' \

diff --git a/tests/tims.sh b/tests/tims.sh
@@ -7,7 +7,7 @@ echo TIMS TMT16, noms1quant
 name=tims_tmt16
 baseresults=test_output/${name}
 cat "${testdir}/tims_mzmls.txt" | envsubst > test_output/mzmldef
-nextflow run -resume -profile test ${repodir}/main.nf --name ${name} --outdir ${baseresults} \
+$NXFCMD --name ${name} --outdir ${baseresults} \
     --sampletable "${testdir}/tmt16_samples.txt" \
     --noms1quant \
     --input test_output/mzmldef \

diff --git a/tests/tmt16.sh b/tests/tmt16.sh
@@ -10,12 +10,14 @@ name=tmt16denomdeq
 resultsdir=test_output/${name}
 mkdir -p $resultsdir
 cat "${testdir}/tmt16_mzmls.txt" | envsubst > ${resultsdir}/mzmldef
-nextflow run -resume -profile test ${repodir}/main.nf --name ${name} --outdir ${resultsdir} \
+$NXFCMD --name ${name} --outdir ${resultsdir} \
     --input ${resultsdir}/mzmldef \
     --sampletable "${testdir}/tmt16_samples.txt" \
     --hardklor --isobaric '0set-A:tmtpro:126:131N' \
     --tdb "${testdata}/tmt16_fa.fa" \
     --mods 'carbamidomethyl;oxidation;43.005814,*,opt,N-term,Unknown' \
+    --maxmiscleav 2 \
+    --pepconflvl 0.05 \
     --deqms --keepnapsmsquant --genes
 
 
@@ -25,7 +27,7 @@ baseresults=${resultsdir}
 resultsdir=test_output/${name}
 mkdir -p $resultsdir
 cat <(head -n1 "${testdir}/tmt16_mzmls.txt") <(grep fr07 ${testdir}/tmt16_mzmls.txt) | envsubst > ${resultsdir}/mzmldef
-nextflow run -resume -profile test ${repodir}/main.nf --name ${name} --outdir test_output/${name} \
+$NXFCMD --name ${name} --outdir test_output/${name} \
     --input ${resultsdir}/mzmldef \
     --sampletable "${testdir}/tmt16_samples.txt" \
     --hardklor --isobaric '0set-A:tmtpro:126:131N' \
@@ -48,7 +50,7 @@ resultsdir=test_output/${name}
 mkdir -p $resultsdir
 cat "${testdir}/tmt16_mzmls.txt" | envsubst > ${resultsdir}/oldmzmls
 cat "${testdir}/tmt16_setB_mzmls.txt" | envsubst > ${resultsdir}/mzmldef
-nextflow run -resume -profile test ${repodir}/main.nf --name ${name} --outdir test_output/${name} \
+$NXFCMD --name ${name} --outdir test_output/${name} \
     --input ${resultsdir}/mzmldef \
     --sampletable "${testdir}/tmt16_setAB_samples.txt" \
     --isobaric '0set-A:tmtpro:126:131N set-B:tmt16plex:126:131N' \
@@ -69,7 +71,7 @@ baseresults=${resultsdir}
 resultsdir=test_output/${name}
 mkdir -p $resultsdir
 cat <(head -n1 "${testdir}/tmt16_mzmls.txt") <(grep fr07 ${testdir}/tmt16_mzmls.txt) <(grep fr08 ${testdir}/tmt16_mzmls.txt | cut -f1-3) | envsubst > ${resultsdir}/mzmldef
-nextflow run -resume -profile test ${repodir}/main.nf --name ${name} --outdir test_output/${name} \
+$NXFCMD --name ${name} --outdir test_output/${name} \
     --input ${resultsdir}/mzmldef \
     --sampletable "${testdir}/tmt16_samples.txt" \
     --hardklor --isobaric '0set-A:tmtpro:126:131N' \
@@ -85,7 +87,7 @@ name=tmt16_singlefile
 resultsdir=test_output/${name}
 mkdir -p $resultsdir
 cat <(head -n1 ${testdir}/tmt16_mzmls.txt) <(grep fr08 ${testdir}/tmt16_mzmls.txt) | envsubst > ${resultsdir}/mzmldef
-nextflow run -resume -profile test ${repodir}/main.nf --name ${name} --outdir test_output/${name} \
+$NXFCMD --name ${name} --outdir test_output/${name} \
     --input ${resultsdir}/mzmldef \
     --sampletable "${testdir}/tmt16_samples.txt" \
     --hardklor --isobaric '0set-A:tmtpro:126:131N' \

diff --git a/tests/tmt16_18.sh b/tests/tmt16_18.sh
@@ -6,7 +6,7 @@ echo TMT 16/18 mix, multi DB run
 name=tmt16_18mix
 baseresults=test_output/${name}
 cat "${testdir}/tmt16_mzmls.txt" <(sed 's/0set-A/20set-A/' "${testdir}/tmt18_mzmls.txt" | tail -n+2) | envsubst > test_output/mzmldef
-nextflow run -resume -profile test ${repodir}/main.nf --name ${name} --outdir ${baseresults} \
+$NXFCMD --name ${name} --outdir ${baseresults} \
     --input test_output/mzmldef \
     --sampletable "${testdir}/tmt18_setAB_samples.txt" \
     --isobaric '0set-A:tmt16plex:126:131N 20set-A:tmt18plex:131' \

diff --git a/tests/tmt16_fast.sh b/tests/tmt16_fast.sh
@@ -1,16 +1,17 @@
 #!/usr/bin/env bash
 
+# Single test to not spend too much time, tests a lot of things but not all.
+
 set -eu
 
 echo TMT16 test with hiRIEF, isobaric and Phospho
-# no hirief, so it can be added in the addsetB test even if not used here
 # Test TMT16, DEqMS w denominator, keepnapsmsquant, implicit normalizing (deqms forces normalize)
 # Warning: no decoys for any set (aka only setA)
 name=tmt16denomdeq
 resultsdir=test_output/${name}
 mkdir -p $resultsdir
 cat "${testdir}/tmt16_mzmls.txt" | envsubst > ${resultsdir}/mzmldef
-nextflow run -resume -profile test ${repodir}/main.nf --name ${name} --outdir ${resultsdir} \
+$NXFCMD --name ${name} --outdir ${resultsdir} \
     --input ${resultsdir}/mzmldef \
     --sampletable "${testdir}/tmt16_samples.txt" \
     --hardklor --isobaric '0set-A:tmtpro:126:131N' \

diff --git a/tests/tmt18.sh b/tests/tmt18.sh
@@ -11,7 +11,7 @@ echo TMT18 phos, no MS1 found somehow
 name=tmt18phos
 baseresults=test_output/${name}
 cat "${testdir}/tmt18_mzmls.txt" | envsubst > test_output/mzmldef
-nextflow run -resume -profile test ${repodir}/main.nf --name ${name} --outdir ${baseresults} \
+$NXFCMD --name ${name} --outdir ${baseresults} \
     --input test_output/mzmldef \
     --sampletable "${testdir}/tmt18_samples.txt" \
     --hardklor --isobaric '0set-A:tmt18plex:126:131N' \
@@ -30,7 +30,7 @@ mkdir -p test_output/${name}
 ln -fs "${testdata}/tmt18_fr06_1000.mzML" "${testdata}/linked_tmt18_fr06_1000.mzML"
 cat "${testdir}/tmt18_mzmls.txt" | envsubst > test_output/${name}/oldmzmls
 sed 's/tmt18_fr/linked_tmt18_fr/;s/0set-A/20set-A/' "${testdir}/tmt18_mzmls.txt" | envsubst > test_output/mzmldef
-nextflow run -resume -profile test ${repodir}/main.nf --name ${name} --outdir test_output/${name} \
+$NXFCMD --name ${name} --outdir test_output/${name} \
     --input test_output/mzmldef \
     --sampletable "${testdir}/tmt18_setAB_samples.txt" \
     --hardklor --isobaric '0set-A:tmt18plex:sweep 20set-A:tmt18plex:sweep' \
@@ -52,7 +52,7 @@ echo TMT18 rerun with different settings post PSMs, --noms1quant
 name=tmt18phos_rerun
 mkdir -p test_output/${name}
 cat "${testdir}/tmt18_mzmls.txt" | envsubst > test_output/${name}/oldmzmls
-nextflow run -resume -profile test ${repodir}/main.nf --name ${name} --outdir test_output/${name} \
+$NXFCMD --name ${name} --outdir test_output/${name} \
     --sampletable "${testdir}/tmt18_samples.txt" \
     --isobaric '0set-A:tmt18plex:131' \
     --tdb "${testdata}/tmt18_fa.fa" \