Here is an example of using multiple COPY operators for JOINKEYS applications that preprocess different input files in different ways:

//CPYJK EXEC PGM=ICETOOL
//TOOLMSG DD SYSOUT=*
//DFSMSG DD SYSOUT=*
//IN1 DD DSN=MY.IN1,DISP=SHR
//IN2 DD DSN=MY.IN2,DISP=SHR
//IN3 DD DSN=MY.IN3,DISP=SHR
//OUT1 DD SYSOUT=*
//OUT2 DD SYSOUT=*
//TOOLIN DD *
* First COPY operator with JOINKEYS application.
COPY JKFROM TO(OUT1) USING(CTL1)
* Second COPY operator with JOINKEYS application.
COPY JKFROM USING(CTL2)
/*
//CTL1CNTL DD *
* JOINKEYS application control statements for first COPY operator.
  JOINKEYS F1=IN1,FIELDS=(5,12,A),TASKID=T1
  JOINKEYS F2=IN2,FIELDS=(11,12,A),TASKID=T1
  JOIN UNPAIRED
  REFORMAT FIELDS=(F1:4,40,F2:15,20),FILL=C'$'
* Main task control statements for first COPY operator
* (operates on joined records).
  INCLUDE COND=(8,1,CH,EQ,C'Y')
/*
//CTL2CNTL DD *
* JOINKEYS application control statements for second COPY operator.
  JOINKEYS F1=IN1,FIELDS=(5,12,A),TASKID=T1
  JOINKEYS F2=IN3,FIELDS=(9,12,A),TASKID=T2,SORTED
  REFORMAT FIELDS=(F1:4,40,F2:7,20)
* Main task control statements for second COPY operator
* (operates on joined records).
  OUTFIL FNAMES=OUT2,HEADER1=('Analysis Report'),REMOVECC
/*
//T1F1CNTL DD *
* Control statements for subtask1 (F1=IN1) of both COPY operators.
* Subtask1 sorts/joins on 5,12,A automatically
* per JOINKEYS statement for TASKID=T1/F1=IN1.
  INCLUDE COND=(21,3,CH,EQ,C'J82')
  SUM FIELDS=NONE
/*
//T1F2CNTL DD *
* Control statements for subtask2 (F2=IN2) of first COPY operator.
* Subtask1 sorts/joins on 11,12,A automatically
* per JOINKEYS statement for TASKID=T1/F2=IN2.
  OPTION SKIPREC=1
  INCLUDE COND=(25,3,CH,EQ,C'J82')
/*
//T2F2CNTL DD *
* Control statements for subtask2 (F2=IN3) of second COPY operator.
* Subtask1 copies/joins on 9,12,A automatically
* per JOINKEYS statement for TASKID=T2/F2=IN3/SORTED.
  INCLUDE COND=(5,3,CH,EQ,C'J82')
/*