diff --git a/modules/kallisto/index/main.nf b/modules/kallisto/index/main.nf
index 00ae9601..801f339e 100644
--- a/modules/kallisto/index/main.nf
+++ b/modules/kallisto/index/main.nf
@@ -36,7 +36,7 @@ process KALLISTO_INDEX {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(kallisto 2>&1 | sed 's/^kallisto //; s/Usage.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(kallisto 2>&1) | sed 's/^kallisto //; s/Usage.*\$//')
     END_VERSIONS
     """
 }
diff --git a/modules/kallisto/index/meta.yml b/modules/kallisto/index/meta.yml
index ba4855b0..6080eb77 100644
--- a/modules/kallisto/index/meta.yml
+++ b/modules/kallisto/index/meta.yml
@@ -1,7 +1,7 @@
 name: kallisto_index
-description: write your description here
+description: Create kallisto index
 keywords:
-  - sort
+  - index
 tools:
   - kallisto:
       description: Quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
diff --git a/modules/kallistobustools/count/main.nf b/modules/kallistobustools/count/main.nf
index 309bd57c..b0dd3a06 100644
--- a/modules/kallistobustools/count/main.nf
+++ b/modules/kallistobustools/count/main.nf
@@ -53,7 +53,7 @@ process KALLISTOBUSTOOLS_COUNT {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(kb 2>&1 | sed 's/^.*kb_python //;s/positional arguments.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
     END_VERSIONS
     """
 }
diff --git a/modules/kallistobustools/ref/main.nf b/modules/kallistobustools/ref/main.nf
index bc9b32f5..c8e02687 100644
--- a/modules/kallistobustools/ref/main.nf
+++ b/modules/kallistobustools/ref/main.nf
@@ -47,7 +47,7 @@ process KALLISTOBUSTOOLS_REF {
 
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
-            ${getSoftwareName(task.process)}: \$(kb 2>&1 | sed 's/^.*kb_python //;s/positional arguments.*\$//')
+            ${getSoftwareName(task.process)}: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
         END_VERSIONS
         """
     } else {
@@ -66,7 +66,7 @@ process KALLISTOBUSTOOLS_REF {
 
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
-            ${getSoftwareName(task.process)}: \$(kb 2>&1 | sed 's/^.*kb_python //;s/positional arguments.*\$//')
+            ${getSoftwareName(task.process)}: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
         END_VERSIONS
         """
     }
diff --git a/modules/nanoplot/main.nf b/modules/nanoplot/main.nf
index 86b300f5..e36b2da2 100644
--- a/modules/nanoplot/main.nf
+++ b/modules/nanoplot/main.nf
@@ -39,7 +39,7 @@ process NANOPLOT {
         $input_file
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(NanoPlot --version 2>&1 | sed 's/^.*NanoPlot //; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(NanoPlot --version 2>&1) | sed 's/^.*NanoPlot //; s/ .*\$//')
     END_VERSIONS
     """
 }
diff --git a/modules/pairix/main.nf b/modules/pairix/main.nf
index 684ea7e6..c00af657 100644
--- a/modules/pairix/main.nf
+++ b/modules/pairix/main.nf
@@ -34,7 +34,7 @@ process PAIRIX {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(pairix --help 2>&1 | sed 's/^.*Version: //; s/Usage.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(pairix --help 2>&1) | sed 's/^.*Version: //; s/Usage.*\$//')
     END_VERSIONS
     """
 }
diff --git a/modules/pbccs/main.nf b/modules/pbccs/main.nf
index ccf17cc4..5df852cf 100644
--- a/modules/pbccs/main.nf
+++ b/modules/pbccs/main.nf
@@ -51,7 +51,7 @@ process PBCCS {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(ccs --version 2>&1 | grep -e 'commit')
+        ${getSoftwareName(task.process)}: \$(echo \$(ccs --version 2>&1) | grep 'ccs' | sed 's/^.*ccs //; s/ .*\$//')
     END_VERSIONS
     """
 }
diff --git a/modules/plasmidid/main.nf b/modules/plasmidid/main.nf
index 8be58c57..792b3c12 100644
--- a/modules/plasmidid/main.nf
+++ b/modules/plasmidid/main.nf
@@ -47,7 +47,7 @@ process PLASMIDID {
     mv NO_GROUP/$prefix ./$prefix
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(plasmidID --version 2>&1)
+        ${getSoftwareName(task.process)}: \$(echo \$(plasmidID --version 2>&1))
     END_VERSIONS
     """
 }
diff --git a/modules/raxmlng/main.nf b/modules/raxmlng/main.nf
index 7094eaa7..e3bde2f3 100644
--- a/modules/raxmlng/main.nf
+++ b/modules/raxmlng/main.nf
@@ -36,7 +36,7 @@ process RAXMLNG {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(raxml-ng --version 2>&1 | sed 's/^.*RAxML-NG v. //; s/released.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(raxml-ng --version 2>&1) | sed 's/^.*RAxML-NG v. //; s/released.*\$//')
     END_VERSIONS
     """
 }
diff --git a/tests/modules/kallisto/index/main.nf b/tests/modules/kallisto/index/main.nf
index bab78f51..7c6078f8 100644
--- a/tests/modules/kallisto/index/main.nf
+++ b/tests/modules/kallisto/index/main.nf
@@ -7,7 +7,7 @@ include { KALLISTO_INDEX } from '../../../../modules/kallisto/index/main.nf' add
 workflow test_kallisto_index {
 
     def input = []
-    input = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+    input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     KALLISTO_INDEX ( input )
 }
diff --git a/tests/modules/kallistobustools/count/main.nf b/tests/modules/kallistobustools/count/main.nf
index 4400976a..9172ddfc 100644
--- a/tests/modules/kallistobustools/count/main.nf
+++ b/tests/modules/kallistobustools/count/main.nf
@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { KALLISTOBUSTOOLS_COUNT } from '../../../../modules/kallistobustools/count/main.nf' addParams( options: [args:"--cellranger"] )
+include { KALLISTOBUSTOOLS_COUNT } from '../../../../modules/kallistobustools/count/main.nf' addParams( options: [args:"--cellranger -m 1"] )
 
 workflow test_kallistobustools_count {
 
diff --git a/tests/modules/kallistobustools/ref/main.nf b/tests/modules/kallistobustools/ref/main.nf
index 1ecfa339..31b36d0d 100644
--- a/tests/modules/kallistobustools/ref/main.nf
+++ b/tests/modules/kallistobustools/ref/main.nf
@@ -30,3 +30,4 @@ workflow test_kallistobustools_ref_nucleus {
 
     KALLISTOBUSTOOLS_REF( fasta, gtf, workflow)
 }
+
diff --git a/tests/modules/plasmidid/test.yml b/tests/modules/plasmidid/test.yml
index dd472a72..838af394 100644
--- a/tests/modules/plasmidid/test.yml
+++ b/tests/modules/plasmidid/test.yml
@@ -12,7 +12,6 @@
     - path: output/plasmidid/test/data/test.fna
       md5sum: 503a5e1d4654bb2df19420e211070db3
     - path: output/plasmidid/test/data/test.gbk
-      md5sum: c851bba9da6ec72cce591617067df50b
     - path: output/plasmidid/test/data/test.gff
       md5sum: 3ed8912ee9b0712ca491fa78ff5f4da1
     - path: output/plasmidid/test/data/test.karyotype_individual.txt
@@ -28,7 +27,6 @@
     - path: output/plasmidid/test/database/test.fna
       md5sum: 6b843fe652b4369addb382f61952c3dd
     - path: output/plasmidid/test/database/test.gbk
-      md5sum: 1f7972ecbb868823727157d2c482700d
     - path: output/plasmidid/test/database/test.gff
       md5sum: 7e65da147d0a413020b0d92b7b03ffcd
     - path: output/plasmidid/test/fasta_files/MT192765.1_term.fasta