Merge pull request #82 from KumarLabJax/KLAUS-267-compression-resource-config

Klaus 267 compression resource config

Author: SkepticRaven

nextflow/configs/profiles/sumner2.config

@@ -540,6 +540,15 @@ process {
         errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' }
         maxRetries = 3
     }
+    withLabel: "r_compression" {
+        // Note: These resources are enough for 1-hour 800x800 videos.
+        // TODO: These values should scale to duration and size of video.
+        cpus = 2
+        memory = 2.GB
+        time = 2.hours
+        array = 200
+        errorStrategy = 'ignore'
+    }
 }
 
 executor {

nextflow/modules/compression.nf

@@ -9,7 +9,10 @@
  * @return file Path to compressed video
  */
 process COMPRESS_VIDEO_CRF {
-    label "compression"
+    label "cpu"
+    // Any environment with ffmpeg installed should work here.
+    label "tracking"
+    label "r_compression"
 
     input:
     tuple path(video_file), val(crf), val(keyframe_interval)
@@ -19,7 +22,7 @@ process COMPRESS_VIDEO_CRF {
 
     script:
     """
-    ffmpeg -i ${video_file} -c:v libx264 -pix_fmt yuv420p -preset slow -crf ${crf} -g ${keyframe_interval} -f mp4 ${video_file.baseName}_g${keyframe_interval}_crf${crf}.mp4
+    ffmpeg -i ${video_file} -c:v libx264 -pix_fmt yuv420p -preset veryfast -crf ${crf} -g ${keyframe_interval} -f mp4 ${video_file.baseName}_g${keyframe_interval}_crf${crf}.mp4
     """
 }
 
@@ -38,7 +41,10 @@ process COMPRESS_VIDEO_CRF {
  * @note COMPRESS_VIDEO_CRF will typically produce better videos with a low signal-to-noise ratio.
  */
 process COMPRESS_VIDEO_BR {
-    label "compression"
+    label "cpu"
+    // Any environment with ffmpeg installed should work here.
+    label "tracking"
+    label "r_compression"
 
     input:
     tuple path(video_file), val(bitrate), val(keyframe_interval)
@@ -66,6 +72,8 @@ process COMPRESS_VIDEO_BR {
  * @note Difference videos are useful in comparing changes due to compression.
  */
 process COMPUTE_VIDEO_DIFFERENCE {
+    label "cpu"
+    // Any environment with ffmpeg installed should work here.
     label "tracking"
 
     input: