ali generator slurm script

cluster/makeAli.slurm

+#!/bin/bash
+#SBATCH -J makeAli     # the job's name
+#SBATCH -t 00:20:00       # max. wall clock time 5s
+#SBATCH -n 1         # number of tasks
+#SBATCH -N 1
+#SBATCH -c 10
+#SBATCH -o /projects/project-nieverge/logs/makeAli_%j.out  # output file
+#SBATCH --partition=batch
+
+cd $1
+
+source /sw/apps/imod/current/imodenv
+submfg newst.com
+submfg ctfcorrection.com

processing/mc2FromMDOC.py

@@ -37,6 +37,8 @@ parser.add_argument('-i', '--input', nargs='+', default='.', help='Input MDOC fi
 parser.add_argument('-cv', '--cudaVer', nargs='?', type=int, default=92, help='Override CUDA version. Default 92. Reduce to a lower value if MotionCor2 does not run properly with the installed graphics card.')
 parser.add_argument('-ps', '--patchSize', nargs='?', type=int, default=3, help='Override local alignment patch count. Default 3.')
 parser.add_argument('-b', '--binning', nargs='?', type=int, default=1, help='Output binning. Default 1 (no binning).')
+parser.add_argument('-bfg', '--bFactorGlobal', nargs='?', type=int, default=800, help='Global bFactor. Default 800.')
+parser.add_argument('-bfl', '--bFactorLocal', nargs='?', type=int, default=200, help='Global bFactor. Default 200.')
 parser.add_argument('-dw', '--doseWeight', action='store_true', help='Do dose-weighting on alignment.')
 parser.add_argument('-ss', '--splitSum', action='store_true', help='Split sum saving for cryoCARE.')
 parser.add_argument('-cl', '--correctLines', action='store_true', help='Use correctK2Lines.py script for correcting lines due to drifty camera sensor.')
@@ -209,12 +211,12 @@ for inputFile in args.input:
                 doseWeightParams = ""
 
             scriptFile.write("echo Aligning frame stack %s \n" % (os.path.join(sourceDir, imageParams['filename']) ))
-            scriptFile.write("MotionCor2-cuda%i -InMrc \"%s\" -OutMrc \"%s\" -Patch %i %i \
-             -InFmMotion 0 -Iter 30 -Tilt %f -Group %i -FtBin %i -PixSize %f%s %s\n\n" %(args.cudaVer,
+            scriptFile.write("MotionCor2-cuda%i -InMrc \"%s\" -OutMrc \"%s\" -Patch %i %i -Bft %i %i \
+             -InFmMotion 0 -Iter 10 -Tilt %f -Group %i -FtBin %i -PixSize %f%s %s\n\n" %(args.cudaVer,
                                                                                          os.path.join(sourceDir, imageParams['filename']),
                                                                                          os.path.join(alignedDir, imageParams['filename']),
-                                                                                         args.patchSize,
-                                                                                         args.patchSize,
+                                                                                         args.patchSize, args.patchSize,
+                                                                                         args.bFactorGlobal, args.bFactorLocal,
                                                                                          imageParams['tiltangle'],
                                                                                          args.group,
                                                                                          args.binning,