Description of output files. Part I

docs/output.md

@@ -14,19 +14,21 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) DSL2.
 
 
 ### PREPARE_INPUT
-Here the input YAML is being processed. Thr subworkflow generate the input channels used as by the other subworkflows.</p> 
+Here the input YAML is being processed. This subworkflow generates the input channels used as by the other subworkflows.</p> 
 
 
 ### GENOMESCOPE_MODEL
 <details markdown="1">
   <summary>Output files</summary>
 
-  - <code>model</code>
-    - kmer coverage model
-  - <code>ktab</code>
+  - <code>kmer/*ktab</code>
     - kmer table file
-  - <code>hist</code>
+  - <code>kmer/*hist</code>
     - kmer histogram file
+  - <code>kmer/*model.txt</code>
+    - genomescope model in text format
+  - <code>kmer/*[linear,log]_plot.png</code>
+    - genomescope kmer plots
 
 </details>
 
@@ -39,19 +41,17 @@ This subworkflow generates a KMER database and coverage model used in [PURGE_DUP
 <details markdown="1">
   <summary>Output files</summary>
 
-  - <code>primary_contigs</code>
-    - primary assembly in FASTA format
-  - <code>alternate_contigs</code>
-    - haplotigs in FASTA format
-  - <code>primary_hic_contigs</code>
-    - primary assembly in FASTA format for hifiasm-hic mode
-  - <code>alternate_hic_contigs</code>
-    - haplotigs in FASTA format for hifiasm-hic mode
+  - <code>\*hifiasm\*/*p_ctg.[g]fa</code>
+    - primary assembly in GFA and FASTA format; for more details refer to [hifiasm output](https://hifiasm.readthedocs.io/en/latest/interpreting-output.html) 
+  - <code>\*hifiasm\*/a_ctg.[g]fa</code>
+    - haplotigs in GFA and FASTA format; for more details refer to [hifiasm output](https://hifiasm.readthedocs.io/en/latest/interpreting-output.html)
+  - <code>\*hifiasm\*/*bin</code>
+    - internal binary hifiasm files; for more details refer [here](https://hifiasm.readthedocs.io/en/latest/faq.html#id12)
 
 </details>
 
-Raw assembly(-ies) is generated here. hifiasm is run on the input HiFi reads then raw contigs are converted from GFA into FASTA format.
-In case hifiasm HiC mode is switched on tun hifiasm with HiC data</p> 
+This subworkflow generates a raw assembly(-ies). First, hifiasm is run on the input HiFi reads then raw contigs are converted from GFA into FASTA format, this assembly is due to purging, polishing (optional) and scaffolding further down the pipeline. 
+In case hifiasm HiC mode is switched on, it is performed as an extra step with results stored in hifiasm-hic folder.</p> 
 
 ![Raw assembly subworkflow](https://raw.githubusercontent.com/sanger-tol/genomeassembly/documentation/docs/images/v1/raw_assembly.png)
 
@@ -60,11 +60,12 @@ In case hifiasm HiC mode is switched on tun hifiasm with HiC data</p>
 <details markdown="1">
   <summary>Output files</summary>
 
-  - <code>pri</code>
+  - <code>\*.hifiasm.\*/purged.fa</code>
     - purged primary contigs
-  - <code>alt</code>
+  - <code>\*.hifiasm.\*/purged.htigs.fa</code>
     - haplotigs after purging  
-
+  - other files from the purge_dups pipeline
+    - for details refer [here](https://github.com/dfguan/purge_dups)
 </details>
 
 Retained haplotype is identified in primary assembly. The alternate contigs are updated correspondingly.