Implement feature to run pipelines on h5ad files with different suffixes

Implement logic in channels.nf and files.nf
Add docs

docs/pipelines.rst

@@ -620,6 +620,25 @@ In the generated .config file, make sure the ``file_paths`` parameter is set wit
 
 - The ``suffix`` parameter is used to infer the sample name from the file paths (it is removed from the input file path to derive a sample name).
 
+In case, you want to use multiple .h5ad files that have different suffixes, use the following strategy to define the h5ad param::
+
+    [...]
+    data {
+        h5ad {
+            GROUP1 {
+                file_paths = "[path-to-group1-files]/*.SUFFIX1.h5ad"
+                suffix = ".SUFFIX1.h5ad"
+            }
+            GROUP2 {
+                file_paths = "[path-to-group1-files]/*.SUFFIX2.h5ad"
+                suffix = ".SUFFIX2.h5ad"
+            }
+        }
+    }
+    [...]
+
+Note: GROUP1, GROUP2 are just example names here. They can be replaced by any value as long as they are alphanumeric (underscores are allowed).
+
 ----
 
 Loom

src/channels/channels.nf

@@ -83,10 +83,20 @@ workflow getDataChannel {
             }
         }
         if(params.data.containsKey("h5ad")) {
+            dataH5ad = params.data.h5ad
+            def filePaths = null
+            def suffix = null
+            if(!dataH5ad.containsKey("file_paths") && !dataH5ad.containsKey("suffix")) {
+                filePaths = dataH5ad.collect { k,v -> v["file_paths"] }
+                suffix = dataH5ad.collect { k,v -> v["suffix"] }
+            } else {
+                filePaths = dataH5ad.file_paths
+                suffix = dataH5ad.suffix
+            }
             data = data.concat(
-                getFileChannel( 
-                    params.data.h5ad.file_paths,
-                    params.data.h5ad.suffix
+                getFileChannel(
+                    filePaths,
+                    suffix
                 ).map {
                     it -> tuple(it[0], it[1], "h5ad", "h5ad")
                 }

src/utils/processes/files.nf

@@ -5,8 +5,17 @@ def getBaseName(file) {
 
 def extractSample(path, suffix) {
     // Extract the sample name based on the given path and on the given suffix
-    suffix = suffix.replace(".","\\.")
-    pattern = /(.+)\/(.+)${suffix}/
-    (full, parentDir, id) = (path =~ pattern)[0]
-    return id
+    if(suffix instanceof String)
+        suffix = [suffix]
+    suffix = suffix.collect { it.replace(".","\\.") }
+    for (String sufx : suffix) {
+        pattern = /(.+)\/(.+)${sufx}/
+        res = (path =~ pattern)
+        if(res.size() == 0) continue
+        if(res.size() == 1) {
+            (full, parentDir, id) = res[0]
+            return id
+        }
+    }
+    throw new Exception("VSN ERROR: the suffix params couldn't match any of the file paths. Make sure the suffix param exist in the file paths.")
 }