fix for end of DSL1 support

README.md

@@ -37,6 +37,8 @@ The pipeline uses [Nextflow](http://www.nextflow.io) as the execution backend. P
 
     **Note**: set `-with-singularity` to use Singularity instead of Docker. 
 
+    **Important**: Since release `22.12.0-edge`, DSL1 is not further supported in Nextflow. Until `sqtlseeker2-nf` is migrated to DSL2, the pipeline should be run using an older Nextflow release. This can be done using `NXF_VER` before Nextflow commands, e.g. `NXF_VER=22.04.0 ./nextflow run guigolab/sqtlseeker2-nf -with-docker`.
+
 ## Pipeline usage
 
 Launching the pipeline with the `--help` parameter shows the help message:

ci/ci.sh

@@ -8,7 +8,7 @@ case "$1" in
   run)
     shift
     echo "Running test pipeline..." >&2
-    nextflow run . -resume -with-docker --dir ${OUT_DIR} $@
+    NXF_VER=22.04.0 nextflow run . -resume -with-docker --dir ${OUT_DIR} $@
     md5sum ${OUT_DIR}/*/*/*
     ;;
   validate)

ci/md5s.txt

@@ -1,4 +1,4 @@
-aa57acbed1d74ea757cf7f1132eae083  ci/groups/tissue1/all-tests.nominal.tsv
-e7c296d0d083a991ae151eac21cc6b03  ci/groups/tissue1/sqtls-0.05fdr.nominal.tsv
-fdc4615294b9ee2bd091b6f36ca1540d  ci/groups/tissue2/all-tests.nominal.tsv
-ec9152800ee2f5ff7bc037dba05c2049  ci/groups/tissue2/sqtls-0.05fdr.nominal.tsv
+b16a3de2da33adfb7ada45ed00ab6659  ci/groups/tissue1/all-tests.nominal.tsv
+16b0f79c00b22c56da9213797b5eb0df  ci/groups/tissue1/sqtls-0.05fdr.nominal.tsv
+b68e676313556f1757c43daa7671111c  ci/groups/tissue2/all-tests.nominal.tsv
+a8d78074279b4aca92f4193ea5334b1f  ci/groups/tissue2/sqtls-0.05fdr.nominal.tsv