Address review comments

CITATIONS.md

@@ -42,7 +42,7 @@
 
 - [CheckM2](https://doi.org/10.1038/s41592-023-01940-w)
 
-  > Chklovski, A., Parks, D. H., Woodcroft, B. J., & Tyson, G. W. (2023). CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nature Methods, 20(8), 1203-1212.
+  > Chklovski, A., Parks, D. H., Woodcroft, B. J., & Tyson, G. W. (2023). CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nature Methods, 20(8), 1203-1212. doi: https://doi.org/10.1038/s41592-023-01940-w
 
 - [Chopper](https://doi.org/10.1093/bioinformatics/bty149)
 

docs/output.md

@@ -596,7 +596,7 @@ If the parameter `--save_checkm_reference` is set, additionally the used the Che
 
 </details>
 
-If the parameter `--save_checkm2_reference` is set, the CheckM2 reference datasets will be stored in the output directory.
+If the parameter `--save_checkm2_data` is set, the CheckM2 reference datasets will be stored in the output directory.
 
 <details markdown="1">
 <summary>Output files</summary>

nextflow_schema.json

@@ -778,12 +778,12 @@
                 "checkm2_db": {
                     "type": "string",
                     "description": "Path to local folder containing already downloaded and uncompressed CheckM2 database (.dmnd file).",
-                    "help_text": "The pipeline can also download this for you if not specified, and you can save the resulting directory into your output directory by specifying `--save_checkm2_data`. You should move this directory to somewhere else on your machine (and supply back to the pipeline in future runs again with `--checkm2_db`."
+                    "help_text": "The pipeline can also download this for you if not specified, and you can save the resulting directory into your output directory by specifying `--save_checkm2_data`. You should move this directory to somewhere else on your machine (and supply back to the pipeline in future runs again with `--checkm2_db`)."
                 },
                 "checkm2_db_version": {
                     "type": "integer",
                     "default": 5571251,
-                    "description": "CheckM2 database version number to download (Zenodo record ID, for reference check https://zenodo.org/records/5571251)."
+                    "description": "CheckM2 database version number to download (Zenodo record ID, for reference check the canonical reference https://zenodo.org/records/5571251, and pick the Zenodo ID of the database version of your choice)."
                 },
                 "save_checkm2_data": {
                     "type": "boolean",

subworkflows/local/bin_qc.nf

@@ -161,7 +161,10 @@ workflow BIN_QC {
         COMBINE_BINQC_TSV(CHECKM_QA.out.output.collect { summary -> summary[1] })
 
         qc_summary = COMBINE_BINQC_TSV.out.combined
-        ch_versions = ch_versions.mix(CHECKM_QA.out.versions.first())
+        ch_versions = ch_versions.mix(
+            CHECKM_QA.out.versions.first(),
+            COMBINE_BINQC_TSV.out.versions
+        )
     }
     else if (params.binqc_tool == "checkm2") {
         /*
@@ -172,7 +175,10 @@ workflow BIN_QC {
         COMBINE_BINQC_TSV(CHECKM2_PREDICT.out.checkm2_tsv.collect { summary -> summary[1] })
 
         qc_summary = COMBINE_BINQC_TSV.out.combined
-        ch_versions = ch_versions.mix(CHECKM2_PREDICT.out.versions.first())
+        ch_versions = ch_versions.mix(
+            CHECKM2_PREDICT.out.versions.first(),
+            COMBINE_BINQC_TSV.out.versions
+        )
     }
 
     if (params.run_gunc) {