WIP: Modules updates and docs fixes

README.md

@@ -33,12 +33,12 @@ Main steps:
 
   <details>
       <summary><strong>Guide Tree</strong> (Optional)</summary>
-      <p>Renders a guide tree with a chosen tool (list available in <a href="docs/usage.md#2-guide-trees">usage</a>). Some aligners use guide trees to define the order in which the sequences are aligned.</p>
+      <p>Renders a guide tree with a chosen tool (list available in <a href="https://nf-co.re/multiplesequencealign/usage.md#2-guide-trees">usage</a>). Some aligners use guide trees to define the order in which the sequences are aligned.</p>
   </details>
 
   <details>
       <summary><strong>Align</strong> (Required)</summary>
-      <p>Aligns the sequences with a chosen tool (list available in <a href="docs/usage.md#3-align">usage</a>).</p>
+      <p>Aligns the sequences with a chosen tool (list available in <a href="https://nf-co.re/multiplesequencealign/usage.md#3-align">usage</a>).</p>
   </details>
 
   <details>
@@ -53,7 +53,7 @@ Main steps:
 
 <br>
 
-More introctory material: [talk](https://www.youtube.com/watch?v=suNulysHIN0) from the nextlow summit, [poster](docs/images/poster-nf-msa.pdf).
+More introductory material: [talk](https://www.youtube.com/watch?v=suNulysHIN0) from the nextlow summit, [poster](https://github.com/nf-core/multiplesequencealign/blob/dev/docs/images/poster-nf-msa.pdf).
 
 ![Alt text](docs/images/nf-core-msa_metro_map.png?raw=true "nf-core-msa metro map")
 
@@ -235,7 +235,7 @@ Which resources is the pipeline using? You can find the default resources used i
 
 If you are using specific profiles, e.g. [test](conf/test.config), these will overwrite the defaults.
 
-If you want to modify the needed resources, please refer [usage](https://nf-co.re/multiplesequencealign/dev/docs/usage/#custom-configuration).
+If you want to modify the needed resources, please refer [usage](https://nf-co.re/multiplesequencealign/docs/usage/#custom-configuration).
 
 ## Pipeline output
 

bin/shiny_app/shiny_app.py

@@ -66,8 +66,8 @@ def merge_aligner_args(row):
     "seqlength_mean": "Mean Sequence Length",
     "realtime_tree": "Tree Building Time (min)",
     "realtime_aligner": "Alignment Time (min)",
-    "vmem_tree": "Tree Building Memory (GB)",
-    "vmem_aligner": "Alignment Memory (GB)",
+    "rss_tree": "Tree Building Memory (GB)",
+    "rss_aligner": "Alignment Memory (GB)",
     "plddt": "Average pLDDT",
     "NiRMSD": "NiRMSD",
     "aligner": "Assembly",

conf/test_full.config

@@ -15,6 +15,12 @@ process {
         memory: '15.GB',
         time: '4.h'
     ]
+
+    withName: "LEARNMSA_ALIGN"{
+        memory : '20.GB'
+        time   : '4.h'
+        cpus   : 4
+    }
 }
 
 

docs/usage.md

@@ -28,7 +28,7 @@ work                # Directory containing the nextflow working files
 ```
 
 :::note
-We have a lot of use cases examples under [FAQs]("https://nf-co.re/multiplesequencealign/usage/FAQs)
+We have a lot of use cases examples under [FAQs](https://nf-co.re/multiplesequencealign/usage/FAQs)
 :::
 
 ## Samplesheet input

modules.json

@@ -110,7 +110,7 @@
                     },
                     "tcoffee/align": {
                         "branch": "master",
-                        "git_sha": "3e548877f25a5980a177cc4f81d2d2e8c24164ef",
+                        "git_sha": "6c2b47b2e26cf091cfce73658709823675833978",
                         "installed_by": ["modules"]
                     },
                     "tcoffee/alncompare": {
@@ -136,7 +136,7 @@
                     },
                     "tcoffee/regressive": {
                         "branch": "master",
-                        "git_sha": "66b22564bc1bc0db7292f2073cdef954ead773e7",
+                        "git_sha": "6c2b47b2e26cf091cfce73658709823675833978",
                         "installed_by": ["modules"]
                     },
                     "tcoffee/seqreformat": {

subworkflows/local/utils_nfcore_multiplesequencealign_pipeline/main.nf

@@ -355,6 +355,9 @@ def saveMapToCsv(List<Map> data, String fileName) {
         row.values().join(',')
     }.join('\n')
 
+    // make sure that the null are replaced by empty strings
+    csvContent = csvContent.replaceAll("null", "")
+
     // Write headers and CSV content to the specified file
     new File(fileName).withWriter { writer ->
         writer.write(headers + '\n' + csvContent + '\n')

workflows/multiplesequencealign.nf

@@ -145,12 +145,6 @@ workflow MULTIPLESEQUENCEALIGN{
                 .map { it -> [ [ id: params.pdbs_dir.split("/")[-1].split("\\.")[0] ], it ] }
                 .groupTuple(by: 0)
                 .set { ch_optional_data }
-            if(!params.skip_pdbconversion){
-                CUSTOM_PDBSTOFASTA(ch_optional_data)
-                ch_versions = ch_versions.mix(CUSTOM_PDBSTOFASTA.out.versions)
-                ch_seqs = CUSTOM_PDBSTOFASTA.out.fasta
-            }
-
 
         }else{
             // Identify the sequence IDs from the input fasta file(s)