[Do not merge!] Pseudo PR for first release

README.md

@@ -72,7 +72,11 @@ For more details about the output files and reports, please refer to the
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
-- [Mahdi Mohammed](https://github.com/U13bs1125): ported the original pipeline to _nf-core_ template 2.14.x.
+- [Mahdi Mohammed](https://github.com/U13bs1125) ported the original pipeline to _nf-core_ template 2.14.x.
+- [Martin Frith](https://github.com/mcfrith/), the author of LAST, gave us extensive feedback and advices.
+- [Michael Mansfield](https://github.com/mjmansfi) tested the pipeline and provided critical comments.
+- [Aleksandra Bliznina](https://github.com/aleksandrabliznina) contributed to the creation of the initial `last/*` modules.
+- [Jiashun Miao](https://github.com/miaojiashun) and [Huyen Pham](https://github.com/ngochuyenpham) tested the pipeline on vertebrate genomes.
 
 ## Contributions and Support
 

assets/multiqc_config.yml

@@ -19,10 +19,39 @@ custom_data:
     file_format: "tsv"
     section_name: "Training parameter statistics"
     plot_type: "table"
+    headers:
+      id:
+        title: "ID"
+        description: "target___query"
+      substitution_percent_identity:
+        title: "Substitution Percent Identity"
+      "last -t":
+        title: "Temperature"
+        description: "Parameter for converting between scores and probability ratios. This affects the column ambiguity estimates. A score is converted to a probability ratio by this formula: exp(score / TEMPERATURE). The default value is 1/lambda, where lambda is the scale factor of the scoring matrix, which is calculated by the method of Yu and Altschul (YK Yu et al. 2003, PNAS 100(26):15688-93)."
+      "last -a":
+        title: "Gap existence"
+        description: "Gap existence cost (lastal -a)"
+      "last -b":
+        title: "Gap extension"
+        description: "Gap extension cost (lastal -b)"
+      "last -A":
+        title: "Insertion existence"
+        description: "Insertion existence cost (lastal -A)"
+      "last -B":
+        title: "Insertion extension"
+        description: "Insertion extension cost (lastal -B)"
   last_o2o:
     file_format: "tsv"
     section_name: "Alignment statistics"
     plot_type: "table"
+    headers:
+      id:
+        title: "ID"
+        description: "target__query"
+      TotalAlignmentLength:
+        title: "Total alignment length"
+      PercentSimilarity:
+        title: "Percent similarity"
 
 sp:
   last_o2o:

docs/usage.md

@@ -47,12 +47,6 @@ Please see the [parameter documentation](https://nf-co.re/pairgenomealign/parame
 
 - The `last-train` commands runs with `--revsym` as the DNA strands play equivalent roles in the studied genomes.
 
-- The `lastdb` command takes all CPU cores available (`lastdb -P0`). Note that
-  when using more than one core, the output of `lastdb` may vary, causing the
-  order of tied positions to change. To prevent this to happen, you can pass a
-  nextflow parameter file to the pipeline that reduces the number of CPUs
-  allocated to `LAST_LASTDB` to 1.
-
 ## Running the pipeline
 
 The typical command for running the pipeline is as follows: